Aryballe Suite Overview

Aryballe Suite is the proprietary software provided with the NeOse Advance used in the acquisition and analysis of odor data.

Computer specifications

The user will need a computer operating under the following minimum requirements:

• Microsoft Windows user account with Administrator rights 
  • 10 Professional (64-bits), build 1809 or higher
  • 11 Professional (64-bits), build 22621 or higher
• 8 GB RAM (16 GB recommended)
• CPU Core i5 Gen 8 or higher (> 2017) 1.6 GHz
• Internet connection
• USB ports: 1 SuperSpeed USB

Operating Conditions

The Aryballe Suite is used to operate the NeOse Advance and its respective accessories. Before launching an experiment, it's important to read the General EHS Guidelines for all Aryballe products as it provides information on operating conditions that may impact your results.

Account Activation

Before you install the Aryballe Suite for the first time, make sure that you have activated your Okta account. 

Click on the "Activate Okta Account" button in the email that was sent to you by Okta. You will be redirected to the Okta registration page on a Web Browser.  

Once on the Okta activation page, create your password and security questions. Click on the "Create My Account" button to finalize your account creation.

You will be redirected to this page. You can close this tab.

This procedure will need to be repeated for each new user account created in your organization. If you have any questions about account set up, please contact support@aryballe.com.

Aryballe Suite installation procedure

1. Download the Aryballe Suite Setup program using the link provided via email from the Aryballe team.
   
    
2. Double click on the .exe installer and follow the wizard instructions.
   
    
3. You must uninstall any previous version of the Aryballe Suite software before you proceed with the installation. If an older version is installed on your computer, you will not be able to install the new software.
   

1.  A License Agreement window will appear. After reading the agreement, check "I accept the agreement" and click on the "Next" Button.
2. Upon software installation, a setup window will appear. Click on the “Next” button.
   
    
3. The setup window lists the components that will be installed. Click on the “Install” button.
4. The installation displays the following window once complete, click on the "Finish" button.
   
   
    
5. The Aryballe Suite Software will appear in your computer's list of applications. By clicking on the Windows icon, you will be able to open the application interface. "Aryballe Suite" allows you to both launch experiments with NeOse Advance and analyze your data from the cloud-based TSDB (Time Series Database). "Aryballe Analysis (local only)" lets you analyze data in your local database.

    6. Open the "Aryballe Suite" application. A login window will open. Use your email as username and the password you have created on the Okta platform. 

 

Once you log in, the application home page will open. The software bundle includes two major modules:

• the Acquisition Module —  to run batch odor acquisitions and to generate diagnostic and analysis reports
• the Answers Module —  to blazing fast and easy odor comparisons with straightforward pass/fail result
• Settings — to see your account and to access device maintenance features (core sensor swap)

Note: It is not possible to run two instances of the application. If you try to open the application when it is already running, a warning pop-up window will open.
  

Acquisition Module Overview

The Acquisition module executes protocols provided with the NeOse Advance. While pre-defined, the protocols can be customized to adjust experimental conditions.

The home page of the Acquisition module is organized in 3 parts:

• List of devices: list of the device that can be used. 
• List of accessories: list of the accessories connected to the computer. Refresh button update both lists. 
• List of protocols: list of the different experimental protocols that can be applied to samples (Odor Acquisition, Calibration & Checks according to the accessories associated). A short description of the protocol is provided upon hover.

Answers (Comparison) Module Overview

The Answers Module is designed for getting a quick answer to these common odor-related questions:

• Do the odors smell the same?
• Do they smell with the same strength?

This tool provides a quick means of comparing samples. It was primarily designed for the use in Quality Control where a fast and reliable odor assessment is often needed. A first rough result can be obtained in less than 2 minutes and a robust, statistically-proven one - in 7-10 minutes.

In order to proceed, you will only need a pair of samples and NeOse Advance. All measures are made in interactive mode to assure the result is obtained in minimum delay.

Live Data View and Annotator

The Live Data View allows users to see data measured by sensors during a run in real time, while the Annotator Tool allows users to add contextual information to the captured data during the experiment. These two tools can be accessed either within the Aryballe Suite application or in an internet browser— Aryballe supports Chrome and Mozilla Firefox.

Live Data View

The Live Data View shows the visualization of the data captured in real time during acquisition. This versatile tool allows the user to select sensor data to display depending on the use case of interest.

When the Acquisition module is executing a protocol, click on the “Live Data View” button in the left navigation pane.

The Live Data View window will open in another tab of the application and displays visual feedback of the device status.

It is also possible to open the Live Data View in a web browser window by clicking on the "Live Data View" button from your Windows menu.

Note that the web browser window will not open unless a run has been started.
 

The Live Data View is composed of two horizontal panels to simultaneously visualize two types of information.

The top banner displays the name of the device used.

On the left side of the window, users can select the parameters to display, while the right side shows sensor output values and device status information in real-time (with the last value recorded). The colors between the numerical values in the right console and in the diagram are linked.

The top and bottom diagrams are completely independent—any of the available sensors can be selected and magnified for more detail. The vertical red line indicates the point in time across both graphs. All diagrams show only the last 2 minutes by default when no magnification is applied.

The following parameters can be displayed:

• Events: acquisition phases, valve switches, inputs based on annotations entered by the user in the Annotator.
• Odor Signature: a normalized odor signature based on Aryballe’s Core Sensor response is generated at a frequency determined in the protocol (at the end of every measure).
• Delta Odor Intensity:the change of odor intensity between the sample measure and the baseline measure (median of all peptides). Same as the Odor Intensity but re-zeroed at the beginning of each acquisition.
• Odor Intensity: the value of odor intensity (median of all peptides) as recorded by Aryballe’s Core Sensor.
• Flow Temperature 1/Humidity 1: displays the value of temperature [°C] and humidity [%] of the sample from the HIH humidity sensor placed after the Aryballe Core Sensor in the fluidic line.

Note: when a sampler is used, the number of the opened inlet is displayed in the event window following the rule:

• 0 is baseline
• 1 is inlet N°1
• 2 is inlet N°2
• Etc.

When an Amplifier is used some parameters are added :

• Amplifier temperature: real-time temperature of the adsorbent. 
• Amplifier power: tension injected for the heating of the trap (normalized value).
• Amplifier setpoint: targeted temperature value (°C).

Annotator Tool

The Annotator Tool allows the operator to add contextual information to a measurement session. Custom events, such as additional information about specific experiments or samples, can be provided by the user in the Custom event annotation field (e.g. Sample name, Comment, Description).

1. When the Acquisition module is executing an experimental plan, click on the “Annotator” button.
2. The annotator window will be opened in a web browser. Click on the “START NEW” button of the Annotator window.
   
   
    
3. A popup window will open so that additional information can be specified. Type in the desired information and click on the “ADD” button.
   
   
    
4. Annotations will be merged with records as tags and will appear as an Event in the Live Data View interface.
   
5. To stop the event, click on the “STOP” button.
   
   
   All annotations that are overlapping a record are indicated as a tag like: $annotation: “custom event” and can be easily seen in the Analysis module browser.

Experiment Analysis Tool Overview

The Experiment Analysis tool enables visualization and statistical analysis of data captured by the solution. The tool works independently from the Acquisition module and can be used without connection to the NeOse Advance device.

The Experiment Analysis tool can be launched from the Aryballe Suite interface in a dedicated tab.

If your installed package includes the Cloud database, you will work with the influxdb Experiment Analysis tool interface.

The homepage of the Experiment Analysis tool is organized according to the different pre-defined protocols:

• Intensity Comparison: (standard and Amplifier)
• Amplifier report: display of odor signatures and statistical analysis when this accessory is used
• Visualization: display of odor signatures and statistical analysis
• Quality Check: validate the device performance
• Cleanliness Check: validate system cleanliness (standard and Amplifier)

The Experiment Analysis tool can also be launched from your Windows menu by clicking on the "Aryballe Analysis (local only)" button. 
 

You will access to the local Experiment Analysis tool interface based on the local database only:

The experiments are organized according to runs, allowing for the selection of a particular experiment and generation of pre-formatted HTML reports. The reports include the entire set of data from Aryballe’s Core Sensor and temperature and humidity sensors.

Clustering Quality Score

CQS is an emerging metric in digital olfaction which provides the best total picture of the sensor’s ability to discriminate specific odors.

Historically, odor sensing performance was difficult to define and evaluate because there was no pre-existing reference for the absolute and widely accepted representation of odors. The adapted way of dealing with this has been to relatively compare molecules to molecules, or odors to odors.

If we assume an odor has no variability, and the sensor to measure this odor is infinitely stable, the measure of this specific stable odor would always generate a signature as an identical point in the N-dimensional space of the sensor. All the recorded odors would be like punctual stars in a sky, separated individually, as below.

As reality is often variable or non-perfect, either due to the protocol of experiment, the odor preparation, or the measurement device itself, these “stars” become fuzzy spots when repeating for a short-term period what should be the same odor measurement. This increases the probability of overlap between odors and increases confusion, hence reducing the resolution, i.e. capability of separating odors. By representing this phenomenon with a numeric value—the Clustering Quality Score—we are able to quantify the degree of separability for these odor data points. The CQS is depending on the distance between the measures of a same odor and the distance with the measures of the N other odors.

CQS allows us to “measure” the performance of a complete experiment, on a continuous scale (from -100% / very bad, to +100% / perfect). There are two different levels of CQS which are relevant to monitor:

• The Global CQS, the score representing the quality of the global separation, i.e. the complete partition. On a set of N different clustered odors, it is represented only by 1 CQS score.
• The Individual CQS, the score representing the quality of each individual cluster (which contains what is supposed to be identical measurements) among the other clusters. On a set of N different clustered odors, it is N different numbers.

The information conveyed by CQS can also be used to measure the repeatability and reproducibility of a technology by looking at records across multiple days for the same device (Repeatability) or by analyzing the score for multiple devices on the same day (Reproducibility).

Connect to Remote Desktop

Prerequisites to connect from user’s computer to remote computer.

On the remote computer’s side:

• It is on and running.
• The Aryballe Suite has been installed on the remote computer.
• All devices and accessories required for the user’s experiments are connected to the remote computer.

On user’s side:

• They have rights to connect to it and know its IP address.
• User’s computer is connected to the same local network as the remote computer, through a VPN if necessary.

1. From user’s computer, open Start menu and search for “Remote Desktop Connection”.
   
   
    
2. Open the application and fill in the IP address:
   
   
    
3. Click on “Show Options” and fill in User name if necessary. The user can also customize the display configuration in the “Display” tab.
   
    
4. Click on connect. Once the connection is made, the user can launch Aryballe Suite as usual.
   
    
5. Whenever the user needs to, he can disconnect from the computer by clicking on the “X” button:
   
   The remote computer will still run the experiment and can be connected to by any users at anytime.

Preparing your experiment

Before starting any experiment, we strongly recommend performing a full system validation to ensure that the system is fully functional and provide traceability for future reference.

 

Fluidic installation

1. NeOse Advance without sampler: environment measurements or sample measurements in a vial which require manual operation from the user.
The set-up will be organized as below, with a PTFE filter on the Baseline inlets of NeOse Advance. 

2. NeOse Advance with sampler: with the use of HeptaValve Mini sampler, automated measurement of up to 7 samples (in vials). The set-up will be organized as below, with a PTFE filter on the Baseline inlets of NeOse Advance and HeptaValve Mini.

3.  NeOse Advance with Amplifier: environment measurements or sample measurements in a vial which require manual operation from the user.
The set-up will be organized as below, with a PTFE filter on the Baseline inlets of NeOse Advance and of the Amplifier. 

4.  NeOse Advance with Amplifier with sampler: with the use of HeptaValve Mini sampler, automated measurement of up to 7 samples (in vials) after amplification. The set-up will be organized as below, with a PTFE filter on the Baseline inlets of NeOse Advance, HeptaValve Mini and the Amplifier.

Device Start Up

Before running any experiment, make sure that a non-sterile PTFE Luer filter is added on NeOse Advance Baseline inlet or any Baseline inlet from bundle accessories such as Heptavalve Mini or Amplifier. When drawing in ambient air, always use a filter to protect the sensor from external particles and pollutions. The PTFE filter should remain on the baseline inlet at all times while the device is operating to avoid premature aging of the sensor.

Allow the device to warm up for at least 30 minutes

1. Connect the NeOse Advance to the computer Super Speed USB port using the USB cable provided. Do not plug the NeOse Advance to a USB hub since it may not receive the power required to operate.

2. Open Aryballe Suite by clicking on the Aryballe Suite App from the Windows menu.

3. Open the Acquisition module by clicking on the "Start a new acquisition" button.

4. Select the device and accessories on the left part of the screen and click on the dedicated warm-up protocol.

If your NeOse Advance device does not appear in the device list, try unplugging and replugging it and pressing the "refresh" button in the bottom of the page.

5. Click on "Next"

6. A dedicated protocol windows will appear as shown below. Press "Run" to start the warm-up process. Follow the instructions on the screen to proceed.

The warm-up protocol will make the NeOse Advance and, optionally, accessories (e.g. HeptaValve Mini or the Amplifier) to perform the necessary steps to start warming the device and prefill the fluidic system. The protocol will typically run for a few minutes after which you will observe the following message:

You can now use the Aryballe Suite freely but it is advised to wait fat least 30 minutes before starting any experiment.

Please note that Aryballe cannot guarantee the quality of records that were obtained after bypassing this warm up time.

System Checks 

Validating System Cleanliness 

This validation step is highly recommended to ensure the system is properly cleaned prior to making any measurement. It helps prevent system contamination and ensures data quality. Aryballe does not guarantee results from experiments performed on dirty systems. During this procedure, make sure that no vials are connected to inlets. 

Cleaning Protocol of the sampler

The cleaning protocol is performed using an external pump box, without connecting the NeOse Advance.

1. Click on the "Aryballe Suite" button in the Windows menu.
   
   
    
2. Click on the “New Acquisition”. 

1. Connect the HeptaValve Mini to the computer using the USB cable provided. Make sure that no vials are connected to sample inlets. Note that several HeptaValve Mini systems can run on the same computer at the same time for this cleaning step.
    
2. In the Acquisition module, click on the “Clean samplers” button.
    
3. A pop-up window will open that details the next steps.When the HeptaValve Mini is connected, the “Discovering samplers” step will launch automatically.
   
   
   
    
4. If no HeptaValve Mini is connected to the computer, the pop-up window will inform you that no sampler was found.
   
   
    
5. Next, connect the USB cable of the external pump box to the computer. Connect the pump box to the HeptaValve Mini by pushing the PTFE tubing pre-assembled with a black Luer connector into the pump box inlet. Press the black button to turn on the pump box.
   
   
   Click on the “I have connected the pump. Start now!” button.
   
   
    
6. The cleaning protocol starts and each step can be followed up in the window.
   
   During the cleaning process, each inlet is alternatively switched on and off and rinsed with air for 6 seconds until the end of the specified cleaning duration.
   
    
7. Click the “Stop cleaning” button to stop the cleaning protocol before the end of the cleaning duration.
   
    
8. Disconnect the PTFE tubing pre-assembled with a black Luer connector of the external pump.
   
    
9. Turn the pump box off.

Check Cleanliness of the sampler

1. Turn on and connect the NeOse Advance to the HeptaValve Mini using the PTFE tubing pre-assembled with a black Luer connector.
   
    
2. Open the Acquisition module by clicking on "New acquisition" button.
3. Make sure you device and your HeptaValve Mini are connected and detected. 
4. Select the protocol “Cleanliness check of external Sampler” on the right part of the screen, and click on the "Next" button.
   
    
5. A window will open allowing to customize the number of cycles and the number of lanes to check. Click on the "Run" button to start the protocol.
   
   
6. The steps for the Cleanliness check can be followed in the window that opens. The process will begin immediately with one measurement performed for each inlet.
   
   It is possible to follow the odor signal in Live Data View or to generate a cleanup report when the Cleanup check process is completed.
   
    
7. Click on the “Live Sensor View” button to assess the system cleanliness in real time. The Live Data View window will open in the dedicated tab of your interface, or you can open the Live Data View in your internet browser (as described in the Live Data View and Annotator paragraph).
   
   
   • If the odor intensity signal presents a peak upon valve switching, then the system is dirty and another cleaning session needs to be done.
     
     
      
   • Once the system is clean, the odor intensity signal should be stable (presented as minor fluctuations with very small intensity value, typically < 0.2 as shown on the Y axis of the chart).
     
     
      
8. At the end of the cycle, the cleanup check procedure is completed. The validation of the end of the experiment appears on the top left of the summary screen.
   
   
    
9. Click on the "Close" button to return to the Selection screen.
   
    
10. Result of the Cleanup procedure can be visualized using the Experiment Analysis tool.

Check Cleanliness of the Amplifier

This validation step is highly recommended to ensure the system is properly cleaned prior to taking any measurement. It helps prevent system contamination and ensures data quality. Aryballe does not guarantee results from experiments performed on dirty systems.

During this procedure, make sure that no vials are connected to any inlet. This protocol allows to make sure that there is no sample pollution remaining on any fluidic line or trapped on the adsorbent from a previous run of experiment. Since the Tenax TA sorbent is in contact with air, even without air flow, some VOCs may bind to Tenax between experiments, through passive diffusion.

1. Connect your NeOse Advance to the Amplifier as described in the Fluidic installation paragraph of this User Manual.
   
    
2. Connect the NeOse Advance and accessories to your computer.
   
    
3. Open the Acquisition module.
   
    
4. Select the device and the protocol “Cleanliness check (with Amplifier)” and click on “Next” button.
   
   
    
5. A window will open, click on “Run” to start the protocol.
   
   
    
6. The steps for the Cleanliness check can be followed in the window that opens. The process will begin immediately with a baseline and a thermo-desorption step without concentration.
   
   
    
7. Click on the “Live Data View” button to assess the system cleanliness in real time.
   
   Once the system is clean, the odor intensity signal should be stable (presented as minor fluctuations with very small intensity value, typically < 0.2 as shown on the Y axis of the chart).
   
   
   If the odor intensity signal presents a peak upon valve switching, then the system is dirty and another cleaning session needs to be done.
   
   
    
8. At the end of the cycle, the cleanup check procedure is completed. Close the window by clicking on the "Close” button.
   
   
    
9. Result of the Cleanup procedure can be visualized using the Experiment Analysis tool.

Sensor Performance Evaluation - Quality Check

Quality Check is performed to assess the performance of the system, which can decrease over time or after pollution events. Three golden reference samples are provided by Aryballe, which should be well detected and discriminated by the NeOse Advance device.

1. Turn on the NeOse Advance and make sure to allow 30 minutes of warm up.
   
    
2. Follow previous instructions about fluidic installation (NeOse Advance associated to the Heptavalve Mini).
   
    
3. Connect the 3 golden reference samples to 3 sample ports of the HeptaValve Mini:
   • Place the extremity of PEEK tubing from the HeptaValve Mini into the reference molecule vials, going through the septum.
   • Place a vent system, such as a flat needle provided, in the septum of each vial.
   • Samples connected to inlets 1, 2 and 3 are measured alternatively so the headspace of each vial can be replenished between 2 measurements.
     
      
4. Open the Acquisition module by clicking on "Start a new acquisition" button.
   
5. Select the connected device.
   
    
6. Select the protocol to run “Quality check” and click on the "Next" button.
   
    
7. In the following window, run parameters can be customized.
   When checking sensor performance with the provided reference molecules GOLD4, GOLD6, GOLD7, Aryballe assigns by default GOLD4 to inlet 1, GOLD6 to inlet 2 and GOLD7 to inlet 3 to enable future performance comparisons. The name of the experimental plan can be customized to make future retrieval easier. Per default, an example is done with A, B and C.
   
   
   
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   Note

   The number of cycles must be defined for the run—a minimum of 3 cycles is recommended, but 10 cycles is the default value for the Quality Check protocol.

   
    
8. Custom tags can be assigned to all records of a run to provide information on experimental setup and conditions that are being applied to the run. Specific tags can be added independently for each inlet.

1. Steps of the Quality check protocol can be tracked in the window that opens. The process begins immediately with one measurement performed for each inlet.
   
    

Click on the “Live Data View” icon to monitor acquisition in real time. The Live Data View window will open in the dedicated tab of your interface, or can be opened in your internet browser (as described in the Live Data View and Annotator sections).

1. 
2. Once the run is finished, the confirmation of the run completion appears in the main window.
   
   
    
3. Click on the "Close" button to return to the Acquisition screen.
   
    
4. When the protocol is completed, disconnect the vials from the inlets by gently pulling the tubing out of each vial and removing the vent system. Disconnect the NeOse Advance from the HeptaValve Mini by unscrewing the Luer lock on the Analyte inlet of the NeOse Advance while turning the connector of the PTFE tubing in the opposite direction. Make sure that the NeOse Advance Luer lock remain tightly screwed and has not become loose in the process so as to prevent any leakage along the fluidic line.
   
    
5. Start a clean-up process as described in the Cleaning protocol section.
   
    
6. The result of the sensor performance evaluation (Quality Check) can be visualized with the Experiment Analysis tool.

To confirm the NeOse Advance is at its optimal performance level, the Clustering Quality Score (CQS) should be considered. If the device is not able to discriminate the golden reference molecules (i.e. CQS < 50%), Aryballe does not guarantee results of future experiments. If this is the case, please contact your Aryballe FAE or support@aryballe.com.

System calibration

Humidity Correction 

Similar to other sensors, Aryballe’s sensor is sensitive to humidity. Humidity Calibration evaluates the reaction of the NeOse Advance to different humidity levels and applies a humidity correction to each biosensor to ultimately minimize the impact of humidity on the odor signal. A minimum of 5 different humidity levels is mandatory, and the sample humidity level should be included in the range of the humidity calibration.

We recommend performing a Humidity Correction every week.

1. Simply connect a vial with a few water droplets (to create humid headspace) to the "sample" lane of the Neose Advance.
   
    
2. Open the Acquisition module by clicking on "Start a new acquisition" button.
   
3. Select the device.
   
    
4. Select the protocol “Humidity correction”.
   
   
    
5. A window to define the run parameters will open to customize the acquisition name. The default duration is 10 seconds.
   As with other protocols in the Runner, custom tags can be added to all the records to further detail the experimental setup and conditions being applied to the run. Click on the "Run" button to start the Humidity Calibration. 
    
6. The Humidity Calibration protocol will start and each step can be followed in the new window opened. The default setting for this protocol is 100 cycles but the minimal number of cycles necessary is 5 corresponding to 5 different levels of humidity. Data can be viewed in real time by clicking on the “Live data view” icon.
   
   
    
7. Once the experiment starts, a pop-up window opens before each measurement to ensure that the user has changed the humidity concentration for the next measurement, either by turning the tap of the dilutor system or by placing a different vial under the inlet 1 of the HeptaValve Mini.
   
   
    
8. When the sample is ready, click on the “Yes” button.
   NOTE: The protocol will not proceed to the next measurement unless the user clicks on the “Yes” button.
   
    
9. Once you click on the "Yes" button, a pop-up window will confirm the action and the protocol will proceed.
   
    
10. Measurement of the baseline starts, followed by measurement of the sample.
    
    
     
11. When sufficient measurement of various humidity levels is done (at least 5 different levels of humidity in the good range), click on the “Abort” button to stop the run before the completion of 100 cycles.

12. The results of the Humidity Calibration, called Humidity Calibration check, can be visualized using the Experiment Analysis tool.

Performing a comparison study with the Answers module

Getting started

1. Click on "New Experiment" button in Comparison activity domain of the app: 
   
    
2. Select the device from the list  on the left and the protocol from the list of the right. If you have any Aryballe accessories attached, unplug them from the PC in order to be able to see the protocol. 
   
    
3. Click on the "Next" button in the top-right corner. The device will take 5-7 seconds to launch its systems. You will hear its pump turn on (if not turned on yet).
   
    
4. The "Instructions Configuration" page will appear. Here you can set up acquisition and algorithm parameters of the study. Most of the parameters have descriptions and some explanations accessible by pointing the mouse on the 🛈 symbol.
5.  
6. 
   
    
7. Some parameters deserve special attention:
   • Confidence level of comparison (N-sigma): 
     • 2 stands for 2-sigma confidence level (95% confidence when comparing samples)
     • 3 stands for 3-sigma confidence level (99% confidence when comparing samples)
     • A separate field is present for intensity and signature comparison confidences.
     • This parameter is used when calculating errors and as T-test's p-value threshold.
   • Interpretation of the result
     • When comparing two samples, one of 3 objective results may appear:
       • samples are assumed similar (p-value > confidence threshold)
       • samples are different (p-value < confidence threshold)
       • N/A - not applicable - case when only 1 replicate is present in one of the sample batches (at least 2 records by sample are needed to perform Student's t-test)
     • This objective result will always be shown. Nevertheless, it is up to the user to define how to interpret each of these objective results. Pass or fail (good or bad) is subjective: both identical and different can be treated as good and vice versa. In order to tell the software how to treat results, use the interpretation of the result parameter:
       • -1 - to treat different as "pass" and identical as "fail"
       • 1 - to treat identical as "pass" and different as "fail"
       • 0 - to avoid interpretation (only objective result will be shown)
     • Note that N/A result is never interpreted.
       
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       Student's t-test

       Student's t-test is a statistical test that is designed to compare two populations of measurements to test whether these populations are statistically significantly different or indistinguishable: Wikipedia
       The result of a t-test is the so-called p-value. Although its formal definition is not quite user-friendly, it is not difficult to make practical use of it. If the resultant p-value is below the defined threshold (e.g. 0.05), then the two populations of samples are different. If it is above the threshold - then the two populations cannot be proven different and thus are assumed as similar.

1. Once you've set the parameters up, press on "Start experiment" button: 
   
    
2. The main comparison dashboard consists in 3 major parts:
   1. reference sample measures
   2. test sample measures
   3. result, interpretation and details widget 
3. Press on "Add reference" to add a measure of a reference sample and "add test" to add a test measure. It is strongly advised to make those measures in alternating manner, for example reference - test - reference - test and not reference - reference - test - test to allow the headspace to be regenerated.
   
    
4. On each measurement, a pop-up window will appear. Here the user is guided through the measurement according to the protocol. Follow the instructions in the window to proceed, for example: 
   
    
5. While the measurement is being acquired, you can go to Live Data View page to monitor the sensor's activity: sections, valve switches, intensity charts: 
    
6. Once the measurement is completed, type the custom name of the sample (the name does not affect comparison algorithm) and press "add measure". This will add the measure to the batch. 
    
7. Only 1 measure in each batch is required in order to extract intensity and signature distances between samples. Statistically-proven objective result is available when there is at least 2 measures in each batch:
   
    

The more replicates of each sample you acquire, the better is the statistics of your result. Point your mouse on the <warn> sign and you will see this type of message: It is up to the user to set the minimum number of samples per batch which can be done in the instruction configuration page. The default (Aryballe advised) number is 5 but users can set up their own quantity (with a minimum of 3). The result is shown in all cases but the warning appears alongside every result on every tab and exported PDF until the required number of samples in each batch is not achieved.

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   Note

   The result is "assumed similar" and is colored green. This could be different if the inverse interpretation would be chosen.

1. The widget on the right has 3 tabs:
   1. Signature - metrics based on signature comparison: 
      • The radar chart represents the olfactive signatures of the 2 samples and is useful to assess how those superpose: when the 2 shapes have more or less same geometry, it indicates that samples are similar (as in the example above); when they partially or fully diverge - this is a indication that odors have smell differently.
      • Distance - distance between the two signatures accompanied with its error, both in absolute and relative (percentage) form.
        
         
      • Student's t-test (in p-value units). If the value is higher than the error threshold, than samples are considered similar; if less than the threshold, then considered as different.The threshold depends on the confidence level which was chosen in step 5:
        • 0.05 (5%) if n-sigma = 2 
        • 0.01 (1%) if n-sigma = 3
          
           
      • Result: "assumed similar" or "different". May be of 3 colors: green, red or black depending on result interpretation (see step 5). Note that green or red decoration depends on the chosen interpretation.  In case of no interpretation, the result will appear black.
        
   2. Intensity - metrics based on odor strength comparison: 
      • Distance - difference in intensities (in radians) between the 2 samples accompanied with its error, both in absolute and relative (percentage) form
        
      • Student's t-test (same principle as in signature comparison, but based on intensity difference and not signature distance)
        
         
      • Result (same principle as in signature comparison but based on intensity difference and not on signature distance). Note that green or red decoration depends on the chosen interpretation .
        
      • The boxplot represents the 2 samples - reference and test. Each "box" represents the sample's population mean, 1st and 3rd quartiles and sometimes min and max horizontal ticks outside the boxes if those are "further" than quartiles. You can only see quartile ticks when having more than 2 samples in the batch.
        
         
   3. Summary table 
2. You can modify some of the instructions at any time by clicking on the Change instructions option in the menu on the top-right. You can tweak algorithm-related parameters but you cannot modify acquisition ones. For this, you will need to restart the experiment
   
3. You can export the results of the experiment at any time. Note that the export will generate a document or data which correspond to the current state of the experiment (currently active measures and parameters). If you change the parameters or select another set of measures, it will alter the shown results and you will need to re-generate the export(s).
   1. PDF export generates a document with all the results in a visual (picture) form
   2. CSV exports generates a folder on you PC with 3 CSV files for:
      • Intensity comparison file
      • Signature comparison file
      • List of measures with intensity and signature numerical values

Loading references from existing database

It is possible to load existing reference measures from an existing database rather than measuring them directly. For this:

1. Click on the Load reference button on the bottom left:  
   
    
2. A  dedicated modal will pop up with the list of previous runs: 
   
    
3. Find the run/batch of interest, open it up with the "+" button on the left and select the items that you want to load as reference. Note that you can also extend the list of all the records for one compound in order to select only the measures of interest, e.g. 
   
    
4. Click on the Load button in the bottom of the modal window.
   
    
5. The selected measures will be added to the references batch as if they were measured directly.
   
    

The Presets system

Presets in the Answers Module enable organizations to pass the relay between the teams: it is up to quality control or R&D engineers to set up the environment, define procedures and tweak the parameters whereas operator's job is to execute the predefined steps, often at scale.

This is where presets come into play. In the Answers module trained personnel can set up the experiment, save it as a preset, then pass it to one or multiple operators for execution. When performing an experiment started with the preset, no parameters - neither acquisition ones nor algorithmic - can be changed. Not even the accessories set.

By default the software has no presets. It is up to the users to create them when the appropriate set of rules is found. In order to create a preset, open the menu on the top-right and select the Save as preset option.

An pop-up window will appear where you can fill-up the preset's name and description

Once the preset is saved, you can continue with the current study. You can also change instructions and save another preset if needed.

The next time you or you colleagues will use the Aryballe Suite, an experiment can be started from the preset. For this, when on Home page, select the Presets menu on the right 

Find the preset of interest and click on the corresponding New experiment button on the right. This will ensure the NeOse and accessories are connected and will directly proceed to the main comparison dashboard avoiding instructions setting up (as they are already set up in the preset itself).

An experiment started "from a preset" has following limitations compared to an experiment "from scratch":

• User cannot modify instructions (they are fixed by the preset)
• User cannot "save as preset" (because it is already loaded from another one)

All the other actions like reference and tests acquisitions, loading from database, PDF and CSV exports are available.

Launching a Batch Acquisition Experiment

Different types of acquisition protocols can be launched according to the device and accessories associated.

As explained in the NeOse Advance section, make sure to warm up the device for a minimum of 30 minutes and to add non-sterile PTFE Luer filters on the Baseline inlets of both the NeOse Advance and the HeptaValve Mini. Also, make sure to warm up the Amplifier for a minimum of 30 minutes and to add non-sterile PTFE Luer filters on the Baseline inlet. 

Generic Acquisition (unique sample) without sampler

The Generic Acquisition Protocol allows for automated data acquisitions of a single named sample without using an HeptaValve Mini. It can be used for on-the-fly sample detection and recognition based on comparison with a previously built odor database. 

1. Open the Acquisition module by clicking on the "Start a new acquisition" button.
   
    
2. Select the device and the protocol “Generic acquisition (unique sample)” and click on the "Next" button.
3. The run can be customized by modifying the name of the plan, the number of cycle, the duration of the analyte acquisition, the pump power and the time between acquisitions. This protocol includes only 1 sample.
   
   
    
4. The sample must be named. Tags can be added by clicking on the "New tag" button, filling out the field and validated by hitting the return key. 
   
   
    
5. Click on the “Run” button to start the experiment.
   
    
6. The Generic Acquisition Protocol (unique sample) will start. Each step can be followed in the new window that opens: step of the measurement, number of cycles. Data can be viewed in real time by clicking on the “Live data view” button on the top right of the screen.
7. You can also open the Live Data View and the Annotator View windows by clicking on the “Live Sensor View” button and on the “Annotator View” button from the dedicated window.  The Live Data View and the Annotator View windows will be opened in your internet browser. 
   

7. Click on the button “Close” to return to the home page.

8. Once the experiment is completed, the confirmation of the end of the experiment appears on the screen. 

 

Generic Acquisition (interactive) without sampler

The Generic Acquisition protocol interactive allows measurement of up to 7 different samples in a run without using an HeptaValve Mini. Data can be analyzed in the Visualization, Recognition or Detection reports.

The absence of an external sampler requires the operator to present and remove each sample at the right time. This interactive protocol guides the operator step by step.

1. Open the Acquisition module by clicking on the "Start a new acquisition" button.
   
    
2. Select the device and the protocol “Generic acquisition (interactive)” and click on the "Next" button.
   
   
    
3. The run can be customized by modifying its name of the plan, the number of cycle, the duration of the analyte acquisition, the pump power, the purge sample line time and the time between acquisitions. 
   
   
    
4. Samples can be added by clicking on the “+ Add sample” button. A maximum of 7 samples can be recorded. You must label each sample, and can add information with individual tags.
   
   
    
5. Prepare the samples to be presented in the same order than indicated in this page from the top to the bottom.
   
    
6. Click on the “Run” button to start the experiment.
   
    
7. The protocol will start. Each step can be followed in the new window that opens. The name of the sample being measured is highlighted with the blue rolling circle and the total number of cycles with the current cycle number appearing on the right.
   
    
8. It is possible to monitor the evolution of several parameters in real time by clicking on the “Live Data View” button.
   
   You can also open the Live Data View and the Annotator View windows by clicking on the “Live Data View” button and on the “Annotator View” button from the dedicated window. The Live Data View and the Annotator View windows will be opened in your internet browser.
   
    
9. Place your sample under the Sample inlet of the device. A message appears before each measurement to ensure that the user has changed the sample to be measured by placing a different vial under the inlet of the NeOse Advance. When the sample is ready, click on the “Yes” button.
   
10. When the sample intake is completed, a message appears at the end of each measurement. Remove your sample from the Sample inlet to ensure that there is no additional sample taken in. When the sample is removed, click on the “Yes” button.
    
11. Once the experiment is completed, the confirmation of the end of the experiment appears on the screen. 
    
12. Click on the button “Close” to return to the home page.
    
     

Generic Acquisition Protocol with sampler

The Generic Acquisition protocol allows measurement of up to 7 different samples in a run. It requires a HeptaValve Mini connected to the NeOse Advance. Data can be analyzed in the Visualization, Recognition or Detection reports.

1. Open the Acquisition module by clicking on the "Start a new acquisition" button.
   
   
    
2. The device and the accessory are displayed if they are connected.
   
    
3. Select the protocol to run “Generic acquisition (with Sampler)”. Click on the "Next" button.
    
4. Run parameters can be customized in the following window, e.g. number of cycles,  acquisition duration and labels for each sample.
   
   
   The name of the experiment can be changed to suit your need of traceability and simpler data browsing.The sample specifics are displayed on the right sequentially from Sample 1 (connected to HeptaValve Mini inlet 1) through Sample 7 (connected to HeptaValve Mini inlet 7).
   
   
    
5. Tags can be added to all samples by clicking on the "New tag" button, filling out the field and validated by hitting the return key. Added tags can be removed by clicking on the cross at right of the tag name.
   
   
    
6. Independent tags can be added for each samples.
   
   
    
7. To measure more samples, click on the “Add sample” button. A maximum of 7 samples can be recorded.
   
    
8. Prepare and connect the samples to the HeptaValve Mini, ensuring that the inlet number matches the samples defined in the run parameters. Tubing from the Heptavalve Mini is placed inside of the vial through the septum and a vent system is added. For more precise instruction, refer to the HeptaValve section of the User Manual.
   
    
9. Click on the “Run” button to start the experiment.
   
    
10. The Generic acquisition protocol will start. Each step can be followed in the new window that opens: sample being measured, step of the measurement, number of cycle.
    
    
     
11. Data can be viewed in real time by clicking on the “Live data view” button on the top right of the screen.
    
     
12. Once the experiment is completed, the confirmation of the end of the experiment appears.
    
    
     
13. Click on the “Close” button to return to the home page.
    
     
14. When the protocol is completed, disconnect the vials from the inlets by gently pulling the tubing out of each vial and removing the vent system. Disconnect the NeOse Advance from the HeptaValve Mini.
    
     
15. Start a clean-up process as described in the section Cleaning protocol section.
    
     
16. Results can be visualized with the Experiment Analysis tool.
    
    
    
    Delete

    Info

    To Abort before the end of the experiment, read the Stopping the Experiment paragraph instructions.

Amplified generic acquisition (interactive) without sampler

The Amplified generic acquisition protocol without sampler allows measurement of up to 7 different samples in a run. It requires an Amplifier connected to the NeOse Advance. The records can be processed in the Amplifier post-analysis modes.

The absence of an external sampler requires the operator to present and remove each sample at the right time. This interactive protocol guides the operator step by step.

1. Open the Acquisition module by clicking on the "Start a new acquisition" button. 
   
    
2. Select the device and the protocol to run “Generic acquisition (interactive with Amplifier)”. Click on the "Next" button.
   
   
    
3. All fields with a red star are mandatory. The run name and number of cycles can be customized.
   
   
    
4. All parameters regarding the behavior of the Amplifier (acquisition time, desorption temperature...) can be customized within the limits defined in the information pop-up.
   
   
    
5. Samples can be added by clicking on the “+ Add sample” button. A maximum of 7 samples can be recorded. Each sample must be named and additional information can be provided with individual tags.
   
   To prevent any confusion during acquisition and subsequent data analysis, samples should be presented by the user in the sequence listed and displayed on the right part of the screen.
   
    
6. Tags can be added to be applied to all samples.
   
   
    
7. Prepare the samples to be presented in the same order than indicated in this page.
   
    
8. Click on the “Run” button to start the experiment.
   
   
    
9. The protocol will start. Each step can be followed in the new window that opens. The name of the sample being measured is highlighted with the blue rolling circle and the total number of cycles with the current cycle number appearing on the right.
   
    
10. It is possible to monitor the evolution of several parameters in real time by clicking on the “Live Data View” button.
    
    
    You can also open the Live Data View and the Annotator View windows by clicking on the “Live Sensor View” button and on the “Annotator View” button from the dedicated window. The Live Data View and the Annotator View windows will be opened in your internet browser.
    
     
11. Place your sample under the Sample inlet of the Amplifier. A message appears before each measurement to ensure that the user has changed the sample to be measured and placed a different vial under the Sample inlet of the Amplifier. When the sample is ready, click on the “Yes” button.
    
    
     
12. When the sample intake is completed, a message appears at the end of each concentration step. Remove your sample from the Sample inlet to ensure that there is no sample taken in during purge. When the sample is removed, click on the “Yes” button.
    
    
     
13. Once the experiment is completed, the confirmation of the end of the experiment appears on the screen. 
    
    
     
14. Click on the button “Close” to return to the home page.
    
     

Amplified acquisition in open environment without sampler

This protocol is fully automatic and allows the user to concentrate and measure a sample periodically for a preset number of times, with no interaction with the user. It is mostly dedicated to low concentration samples (under the limit of detection) or to odors from large, open environments. Purge will thus not be required in this mode.

1. Open the Acquisition module by clicking on the "Start a new acquisition" button.
   
    
2. Select the device and the protocol to run “Open environment acquisition (with Amplifier)”. Click on the "Next" button.
   
3. In the following window, the run can be customized. The number of cycles and the acquisition duration fields must be filled out.
   All Amplifier’s parameters can be customized. Tags can be added.
   
   
    
4. Sample must be named. If necessary, additional individual tags can provide more information. Click on the “+ Add sample” button to add replicates.
   
   
    
5. Click on the "Run" button to start the experiment.
   
    
6. The protocol will start. Each step can be followed in the new window that opens. The name of the sample being measured is displayed next to a waiting icon and the total number of cycles with the current cycle number appearing on the right.
   

It is possible to monitor the evolution of several parameters in real time by clicking on the “Live Data View” button.

You can also open the Live Data View and the Annotator View windows by clicking on the “Live Sensor View” button and on the “Annotator View” button from the dedicated window.  The Live Data View and the Annotator View windows will be opened in your internet browser. 
 

Once the experiment is completed, the confirmation of the end of the experiment appears on the screen. 

 

Click on the button “Close” to return to the home page.

Amplified generic acquisition with sampler

The Amplified generic acquisition protocol allows measurement of up to 7 different samples in a run. It requires both an Amplifier and a HeptaValve Mini connected to the NeOse Advance. The records can be processed in the Amplifier post-analysis modes.

This protocol is fully automated, no human interaction is required once the run is started.

1. Open the Acquisition module by clicking on the "Start a new acquisition" button.
   
    
2. Select the device and the protocol to run “Generic acquisition (with Amplifier & Sampler)”. Click on the "Next" button.
   
   
    
3. All fields with a red star are mandatory. You can customize the run name, and the number of cycles.
   
   
    
4. All parameters regarding the behavior of the Amplifier, (acquisition time, desorption temperature...) can be customized within the limits defined in the information pop-up.
   
   
    
5. You can add samples by clicking on the “+ Add sample” button. A maximum of 7 samples can be recorded. Each sample must be named, and additional information can be provided with individual tags.
   
   The sample labels on the right are displayed in order from inlet 1 through 7. 
   
    

1. Tags can be added to be applied to all samples.
   
   
    
2. Prepare and connect the samples to the HeptaValve Mini, ensuring that the inlet number matches the samples defined in the run parameters. Tubing from the Heptavalve Mini is placed inside of the vial through the septum and a vent system is added.
   
    
3. Click on the "Run" button to start the experiment.
   
    
4. The Generic acquisition protocol will start. Each step can be followed in the new window that opens. The name of the sample being measured is highlighted in dark grey and the total number of cycles with the current cycle number appearing on the right.
   
   
    
5. It is possible to monitor the evolution of several parameters in real time by clicking on the “Live Data View” button.
   
   You can also open the Live Data View and the Annotator View windows by clicking on the “Live Sensor View” button and on the “Annotator View” button from the dedicated window. The Live Data View and the Annotator View windows will be opened in your internet browser. 
   
    

Once the experiment is completed, the confirmation of the end of the experiment appears on the screen. 

 

Click on the button “Close” to return to the home page.

Disconnect the vial from the inlets by gently pulling the tubing out of each vial and removing the vent system and disconnecting the Amplifier from the HeptaValve Mini.

Start a clean-up process.

End of experiment

After each measurement session a thorough system cleaning, as explained in section Cleaning protocol, must be performed to avoid a contaminated system for the next experiment. Aryballe does not guarantee results from experiments performed on dirty NeOse Advance system.

For system cleaning, the NeOse Advance needs to be disconnected. Only the HeptaValve Mini and the external pump box are necessary. During this procedure, make sure that no samples are connected to inlets.

System Shutdown

When the device is clean, shut down the system:

1. Close the Acquisition module window.
   
   
    
2. Close (if opened) the Live Data View and Annotator windows in the browser.
   
    
3. Unplug the NeOse Advance from the computer by removing the USB cable.
   
    
4. Put the transparent caps back on both inlets of the NeOse Advance.

Stopping an Experiment at any time 

1. Click on the “Abort” button to stop the run before the completion of the whole experiment.

 

2. A pop-up window will open. Click on the “Abort” button to validate that you want to abort the experiment.

 

3. The confirmation that you have requested to abort the experiment will appear in the main window.

 

4. The experiment will abort once the measurement currently in process is completed. Click on the "Close" button to return to the Acquisition screen.

Experiment Analysis Tool

The Experiment Analysis tool creates reports for the visualization and analysis of experiments. The humidity correction and/or the drift correction can be applied on the experimental run via this tool.

Before making any statistical analysis, the performance of the device, setup and the calibrations must be verified.

Quality Check

Report Selection

1. In the Aryballe Suite home page, click on the "Analysis and reports" button. Then click on “Start analysis” to open the tool.
   
   
   
    
2. The Experiment Analysis window will open. Click on the “Quality check” button.
   
   
    
3. Select the Quality check run(s) you want to visualize by checking the boxes at the left of the run dates. The number of runs selected will appear in the lower bar.
   
   
    
4. Click on the “Check” button to generate a report.Then two options are offered:
   1. Time labeling: instead of using the standard analyte section, a detected significative odor peak will be used as the analyte. This option is best for Amplifier acquisition.
   2. Exclude first cycle: excluding the entire first cycle from the report is advised for Quality check.
      
      
       
5. Click on “Submit” to generate the report.
6. The report will automatically open in a new browser window and will be saved in the computer under Documents/Aryballe/Quality.

Report Structure

It is possible to select several Quality check runs in the same analysis. The results will be presented run by run in different tabs.

For a selected run, a tab contains:

1. The intensity graph for each cycle and each compound (average and maximum values).

 

1. The CQS score analysis with:
   • The Global CQS, i.e. the score representing the quality of global separation of samples. On a set of N different clustered odors, it is represented only by one CQS score.
   • The Individual CQS, the score representing the quality of each individual cluster (which contains multiple measurements coming from one same sample) among the other clusters. On a set of N different clustered odors, it is represented by N different numbers.
     
     
     A CQS score superior to 50% confirms optimal performance of the sensor.
     
     
      
2. A PCA analysis:
   
   Principal Component Analysis (PCA) is a statistical tool used for multivariate data analysis. In our case, the normalized response of the array of n-biosensors is projected and reduced in a new n-space where the first components explain the majority of the variance between records. Each marker is an acquisition, and each color is a sample. The data points on the two first dimensions plot that are located close to each other indicate a degree of odor proximity, while distant dots indicate different sample odors.
   
   A good performance of the device is indicated by markers of a same color tightly clustering together, while markers of different colors should be clearly separated in different clusters.

System Cleanliness Check of the sampler

Report Selection

1. In the Aryballe Suite main page, click on the "Analysis and reports" button. Then click on “Start analysis” to open the tool.
   
   
    
2. The Experiment Analysis window will open. Click on the “Cleanliness check” button.
   Choose the Cleanliness check run(s) you want to visualize by checking the boxes at the left of the run dates. The number of runs selected will appear in the lower bar.
   
   
   
    
3. Click on the “Check” button to generate a report.
   
   
    
4. The report will automatically open in a new browser window and will be saved in the computer under Documents/Aryballe/Cleanliness.
   
    

Report Structure

The Cleanliness check report is made of as many tabs as there are cycles. One tab represents the measurements of one cycle for all the inlets of the HeptaValve Mini.

The row of tabs allows you to select the cycle. For each cycle, a colored graph represents an inlet.

Each graph is divided in two parts:

• Left is the baseline, delimited by two vertical grey lines.
• Right is the injection of the selected sample, delimited by two vertical blue lines.

The chart represents the average intensity value across all the biosensors and the colored areas delimit the maximum and minimum values.

Validation of the setup’s cleanliness:

• If the odor intensity signal presents a peak upon valve switching (see example below), then the system is dirty and another cleaning session needs to be done
  
• Once the system is clean, the odor intensity signal should be stable (presented as minor fluctuations with very small intensity value, typically < 0.2 as shown on the Y axis of the chart).
  

Visualization Analysis

Report Selection

1. In the Aryballe Suite home page, click on the "Analysis and reports" button. Then click on “Start analysis” to open the tool.
   
   
    
2. The Experiment Analysis window will open. Click on the “Visualization” button to visualize the list of all the runs.
   
    
3. Choose the run(s) you want to visualize by checking the boxes at the left of the run dates. The number of runs selected will appear in the lower bar.
   
   
    
4. Humidity correction can be added to the analysis. Check the boxes at the left of the Humidity Calibration run of interest in the dedicated tab.
   
   
   
    
5. Click on the “Visualize” button to generate a report. Then two options are offered:
   1. Time labeling: instead of using the standard analyte section, a detected significative odor peak will be used as the analyte. This option is best for Amplifier acquisition.
   2. Exclude first cycle: exclude the entire first cycle from the report
6. Submit to start the report generation.
7. The report will automatically open in a new browser window and will be saved in the computer under Documents/Aryballe/Visualization. The .csv documents corresponding to the report are saved automatically at the same location.
   
   
    

Report Structure

At the top of the report, the title, the device name and run id are displayed.

The Visualization report contains the following tabs (described in the sections below):

• Signature
• Evolutions
• Data, displaying PCA charts and Mean relative error matrix
• Sensors
• Time drift
• Humidity correction (if one is applied)
   

Signature: several types of odor signatures are displayed as a radar chart.

• Measured: All raw signatures for every sample and every cycle
• Measured (simplified): Average raw signature over the cycles for each sample (with +/- standard deviation per spot envelope)
• Normalized: All normalized signatures for every sample and every cycle
• Normalized (simplified): Average normalized signature over the cycles for each sample (with +/- standard deviation per spot envelope)
   

Evolutions: Evolution of signature average (with min and max of each signature envelop) over time for each sample. This will include humidity correction if it is applied.

PCA/CQS: Principal Component Analysis (PCA) is a statistical tool used for multivariate data analysis. In our case the normalized response of the array of n-biosensors is projected and reduced in a new n-space where the firsts components explain the majority of the variance between records.

Each marker is an acquisition, and each color is a sample. The data points on the two first dimensions plot that are located close to each other indicate a degree of odor proximity, while distant dots indicate different sample odors. 

PCAs allow to quickly visualize separation of samples. Distant records (represented by a dot) indicate that records are different, while records indistinguishable or close from each other indicate that the measures have an odor proximity. The global CQS, shown on top of the PCA chart indicates how well all samples are separated from each other, while individual CQS shown in the legend at the right of the graph represents how the sample is differentiated form the other samples in the PCA.

Humidity and Temperature: Displays humidity or temperature evolutions over the experiment duration, i.e. the cycles for the baseline and analyte portion of the records. This allows a simple view of the delta in humidity and temperature between the baseline and analyte over time. 

Amplifier cleanliness check

Report selection 

1. In the Aryballe Suite main page, click on the "Analysis and reports" button. Then click on “Start analysis” to open the tool.
   
   
    
2. The Experiment Analysis window will open. Click on the “Amplifier cleanliness check” button.
   
   Choose the Cleanliness check run(s) you want to visualize by checking the boxes at the left of the run dates. The number of runs selected will appear in the lower bar.
   
3. Click on the “Generate” button to generate a report.
   
    
4. The report will automatically open in a new browser window and will be saved in the computer under Documents/Aryballe/Amplifier.
   
    

Report Structure

The Cleanliness check report is made of one Summary and one Amplifier Clean Check tab where you can visualize one graph for each cycle. 

Each graph is divided in two parts:

• Left is the baseline, delimited by the dark discontinous line.
• Right is the thermodesorption measure

Validation of the setup’s cleanliness:

• Without concentration, the thermodesorption signal should be unsignificant as below : 

•  If the peak of thermodesorption is signiticant, meaning that the Tenax is polluted or could had stock VOCs by diffusion during the storage of the Amplifier, redo a cleanliness check of at least 2 cycles.

Amplifier report analysis

Report selection 

1. In the Aryballe Suite main page, click on the "Analysis and reports" button. Then click on “Start analysis” to open the tool.
   
   
    
2. The Runner Experiment Analysis window will open. Click on the “Amplifier” button to visualize the list of all runs.
   
   
    
3. Choose the run(s) you want to visualize by checking the boxes at the left of the run dates. The number of runs selected will appear in the lower bar.
   
   
    
4. Click on the “Generate” button to generate a report.
   
    
5. The report will automatically open in a new browser window shortly after it is generated and will be automatically saved in the computer under Documents/Aryballe/Amplifier.
   
    

Report structure

For selected runs, the Amplifier report provides a Summary tab and as many tabs as there are individual samples. HTML reports are displayed on a web interface such as Mozilla Firefox or Chrome.

Reports are semi-dynamic: you can navigate between panels that will inform you on the discrimination of the records you made, or the intensity of those measurements.

The report window presents the following panels:

Summary : This main panel summarizes the main experimental results.

On the top left chart, the intensities of all the records are displayed, grouped by nature of sample. The intensity appears in radians (rad) and corresponds to the average response across biosensors at the apex of the thermo desorption curve.

The top right chart has a similar organization and presents the area under the selected zone of peak detection. The bottom left chart is a Principal Component Analysis (PCA) representation of the run. Each nature of sample gets its own color, and each sample analyzed gets its own dot on this 2-D chart. The x axis presents the projection of the olfactive signature on the first principal component of the PCA (PC1), and the percentage of expressed variance (59,6% in this example). Similarly, the y axis presents the projection of each record on the second principal component of the PCA (PC2). On this chart, points that appears close have measured olfactive signature that are perceived similar by the sensor, when the furthest points generate the most different signatures.

To ease the reading of this discrimination tool, the bottom right chart presents the global Clustering Quality Score: it is a numerical approach to quantify the performance of discrimination. This value is based on inter- /intra-cluster distances and provides an information on how well samples are clustered and thus discriminated.

You can then further navigate in the individual sample report to see the details of each record by clicking on the name of your sample, where you can then see each thermal desorption cycle per cycle. 

The first temporal data is called a sensorgram: it gives information of the variation of intensity of each biosensor during time. The highlighted green zone is determined automatically by an algorithm and frames the extraction of an olfactive signature, presented in the bottom right. The vertical dotted line indicates the switch of the valve in the Amplifier, corresponding to the beginning of the flow of the adsorbed sample towards the sensor. The second temporal chart presents a red curve corresponding to the temperature of the thermo-desorber, and a blue one recording the amount of humidity during the thermal desorption. A humidity-specific sensor is placed online just after the odor sensor and will monitor the variations of relative humidity of the sample trapped during the concentration. The tables appearing on the top right of the page are numerical informations about the record:

• Apex gives the average intensity of all the biosensors reached on the peak.
• FWHM (Full Width at Height Maximum) gives an information on the width of the peak and is given in seconds.
• Tr is the retention time corresponding to the time to reach the maximum of signal of the peak (seconds). Value is taken after the switch of the injection valve (dotted lines on the chart) and can be characteristic about a chromatographic effect of the peak.
• Area is extracted under the blue zone and is another way to quantify the amount of signal than the Apex value.

Miscellaneous

Log-out procedure

1. Click on Windows Start Button
   
    
2. Use the built-in search bar to find the Credentials Manager, then open it.
   
   
    
3. Choose Windows Credentials
    
   
    
4. In the list of credentials, look for “Aryballe-Suite/<username>” field. In particular case, <username> will be replaced by your account's username, e.g. "Aryballe-Suite/John"
   
    
5. Use the Remove button to delete the credential.
   
   
    
6. Close the Credential Manager.
   
    
7. Restart the Aryballe Suite application and log in again.
   
    
8. You can now use the Aryballe Suite application using the newly logged in account.

Offline Authentication

The Aryballe Suite may be used in an Offline Mode to conform with your organization's IT requirements. Use these instructions if online authentication is not possible on your PC or in your organization. The procedure hass to be performed every time you log out of the application.

Prerequisites

Token file provided by Aryballe is stored on the computer's local drive.

Procedure

1. Open Windows Start Menu.
   
    
2. Open the Aryballe Suite (advanced) folder.
   
    
3. Select Maintenance from the list:
    
   
    
4. Drag and drop the Token file onto the Register offline license item (script) 
   
    
5. A console window will pop up with the following message. 

6. If there is an error message, please contact support@aryballe.com for assistance.

7. Close the console window. You are authenticated with an offline token and can use the Aryballe Suite in offline mode.