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How can I use WorkOut 2.5 with EnVision (offline)?

Document ID: DQ079
Relevant to following products: WorkOut 2.5
Document description: How To: Use WorkOut 2.5 to process measurements made with EnVision



How to use WorkOut 2.5 to process measurements made with EnVision

This document describes how to process measurements with WorkOut 2.5 after measurements have been made by the EnVision software. The document assumes the user has both the EnVision manager (version 1.08 or later) and WorkOut 2.5 software installed on their system.  It is recommended that you follow the steps through in order to fully understand how to setup EnVision and WorkOut 2.5 to work together.

Alternatively an online driver for the EnVision is available from here.

Overview:

  1. Download EnVision import scripts for WorkOut 2.5
  2. Create an EnVision Protocol which outputs the data
  3. Create an EnVision Protocol which outputs the data
  4. Run the EnVision Protocol
  5. Create a WorkOut 2.5 Protocol to import the EnVision data
  6. Refine the WorkOut 2.5 Protocol
  7. Launch the WorkOut 2.5 Protocol
  8. Unsupported EnVision formats
  9.  

    Note: There is some overlap in the terminology used in the two applications, specifically the term “protocol”. Within both WorkOut and the EnVision Manager software the term “protocol” refers to all of the settings for measurements and operations performed before and after measurements. However, each “protocol” is specific to its own application, i.e. EnVision protocols are used within the EnVision manager and WorkOut protocols are within WorkOut only. To avoid confusion this document uses the terms “EnVision Protocol” and “WorkOut Protocol”.


    Download EnVision import scripts for WorkOut 2.5

    Import scripts are required for WorkOut to be able to import data from specific file formats. The latest set of WorkOut 2.5 EnVision import scripts is available for download from here.  Extract the files in the ZIP file to the IScripts sub-directory of your WorkOut 2.5 installation, typically:

    C:\Program Files\Dazdaq\WorkOut 2.5\IScripts

    Now WorkOut 2.5 is setup to automatically recognise and import typical EnVision files.

    Create an EnVision Protocol which outputs the data

    An EnVision protocol is required to take measurements with the EnVision. This EnVision protocol must be setup to take measurements and output the data to a file (which WorkOut can then import).

    The following steps illustrate how to create a typical EnVision protocol and how to set it up to output the results ready for WorkOut to process:

    1. Launch the Wallac EnVision manager.
    2. Expand the Protocols node
    3. Expand Wallac Samples
    4. Right-click the ABS @ 405 node and select Copy
    5. Select the Users node
    6. Right-click and Paste
    7. In the right hand pane: under the Plate tab select all of the wells with the mouse and then choose Select.
    8. Select the Output tab. Here tick the File Output option.  Keep all the other options on this screen as their default.  The default options are as shown here:


    This will automatically create a CSV text file after the measurements are completed. The text file will be created in the location specified under Filename. (The EnVision installation places a short-cut to this default directory on the Windows Desktop).

    Run the EnVision Protocol

    Press Start to take the measurements. When the measurements are completed the EnVision software will automatically create the output file. You can use the short-cut on the Desktop (EnVision Data) to check the file has been created OK. You will note that the new file is in a sub-directory (typically made up of today’s date). If you have Excel installed the file will open in Excel.

    Now that we have an EnVision data file we can setup WorkOut 2.5 to import this data.

    Create a WorkOut 2.5 Protocol to import the EnVision data

    With WorkOut 2.5 you can create a WorkOut protocol which imports data of a particular file format. The wizard uses the installed import scripts to determine how to import a particular data file. When the wizard is finished the resulting protocol can be used to import any data file which follows the same format as the one used in the wizard. This means the protocol can be re-used to import many other data files which follow this format. (It is not necessary to create a new protocol each time you want to import data.)

    The following instructions use the Generic wizard to quickly create a basic protocol which imports the EnVision data file:

    1. Launch WorkOut 2.5
    2. Select Create a new Protocol
    3. Select Import data to analyse from a text file… and press Next.
    4. Press the Browse button and navigate to the newly created file in the EnVision data sub-directory and press OK (or select an EnVision data file to import).
    5. Press Next in the Wizard.  If the Wizard displays the Import Details step you need to specify the File Contents using the controls in the right hand side of the dialogue box. Select the Readings Type as either Endpoint or Kinetic (depending on the data being imported). For 96 well plates select a Plate Width of 12 and a Plate Height of 8. For 384 well plates select a Plate Width of 24 and a Plate Height of 16. The Number of Matrices control should be set to 1 or 2 depending on the data being imported. For data files containing 1 set of data use 1. For data sets such as dual kinetics Fura, FP, UltraLumi, and AlphaScreen with EnVision calculated results, use 2.  Press Next to continue. If the Wizard asks you to choose between two import scripts, select the appropriate script and click Next. The Wizard will then attempt to identify the data file and if successful import the data (if this fails see the section Unsupported EnVision formats below.)
    6. The imported data will be displayed in the next wizard step.
    7. Complete the wizard and make a note of the new WorkOut Protocol name. At the end of the wizard press finish and the new WorkOut Protocol will be launched automatically importing the EnVision data into WorkOut.
    At this point we have created a WorkOut 2.5 Protocol which can import any EnVision data file which uses the same format as the original EnVision data file. The WorkOut 2.5 Protocol has been run for the first time importing the original EnVision data file. This WorkOut 2.5 Protocol can be used to import other EnVision data files of this format.

    Refine the WorkOut 2.5 Protocol

     

    In this example we have used the Generic Wizard to create the protocol. It is likely that you will want to add analyses to process your data as required. Having this first set of data in WorkOut makes it easy to setup the analysis and see the results with your data.

    Now use WorkOut 2.5 to setup the analysis/reporting options as required. For example, you may want to add new transforms. Press Recalculate each time to effect the changes. When you are happy with your settings you can save the Protocol using the File | Save Protocol option. Make a note of the new protocol name.

    Launch the WorkOut 2.5 Protocol

    Now we have a WorkOut 2.5 Protocol which can be used to automatically import EnVision data and process the data as required. 

    This WorkOut Protocol can be launched from WorkOut’s Organiser: using this method you must select which EnVision data file to import. Alternatively WorkOut can be launched from the command line – this maybe useful to import many existing EnVision data files for processing in WorkOut.

    You can also setup the EnVision manager software to use WorkOut 2.5 to process the EnVision data. I.e WorkOut 2.5 can be automatically launched after EnVision measurements are completed from the EnVision manager software. To achieve this:

    1. Open the EnVision Protocol which has been setup to take measurements and output the text file.
    2. Select the Output tab (here is where the File output was ticked previously)
    3. At the bottom of this page of controls you will see an Event box – tick this box.
    4. In the Command enter the path to the WorkOut 2.5 executable. This is the MRunRes.exe in the WorkOut type installation directory, typically:

      C:\Program Files\Dazdaq\WorkOut 2.5\MRunRes.exe

    Under command arguments you must enter the WorkOut Protocol followed by a reference to the output filename produced by the EnVision manager. So for example, if your WorkOut Protocol was called “My Protocol.apr” located in your Protocols directory, you would enter this full path followed by the macro, for example:

    "C:\Documents and Settings\Me\My Documents\My Assays\Protocols\My Protocol.apr"

    You can also optionally use the /exit option to automatically exit WorkOut after the data has been processed.

    Unsupported EnVision formats

    The EnVision is capable of many different types of measurements, including, endpoint, scan, kinetic, multi-label, multi-plate, different plate dimensions (to name a few). It is also capable of exporting the results in many different ways. There are therefore a huge number of different possible configurations and content of data produced in the EnVision output file. It is not feasible for WorkOut 2.5 to be able to automatically recognise and import all of these different possible permutations of data. However, at Dazdaq we have produced several import scripts to deal with the most common scenarios.

    If you require additional import scripts for EnVision data files not currently supported (or for any other instrument) then simply send an example of the text based data file to imports@dazdaq.com and we would be glad to develop a script for you. (WorkOut 2.5’s wizards will optionally write this email for you if it fails to import your data and add it to your Outbox.)





Related articles:
DQ181: Where can I get the latest version of WorkOut 2.0 from?
Downloading the latest version of WorkOut 2.0.

DQ263: Online EnVision driver
Online EnVision driver

DQ174: I want to import time data which uses a different regional separator.
How to: import time data (of the format HH:MM:SS.MS) which uses a different regional separator.

DQ071: My data file cannot be imported
How To: Import data the wizard does not recognise…

DQ041: How do I create an offline assay protocol?
How to: Import data from an existing text file and then analyse it…

DQ042: Can I automate the import process?
How to: Import text files as part of an automated process

DQ050: Can I launch the software from the command line?
How To: Launch the software from the command line.





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