User guide for Assay

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Prerequisites

You have to be in a group member in a Synergy group and user access granted from within Assay. You need to be logged into Synergy to use Assay.

See details in ChemAxon Synergy documentation and the Administration guide for Assay.

Setup tab

In the Setup tab you can define result types (e.g. EC50, Kd etc.) and protocols (experiment descriptions, and referred to as SOP - standard operational protocol). The list of protocols is expandable by administrator users, while result types can be added by users, too.

Protocol

On Protocol tab you can see all protocols (SOPs) that your group is using. To see details about a protocol, click on its row. If you need additional protocols, please contact your Assay administrator.

To create a new protocol click the Add new button in the top right corner. To edit an existing protocol, open the detailed view by clicking on it and click the Edit button . Modify the fields as needed and click the Save button. If you would not like to save the changes, click the X in the top right corner.

You need to provide an Abbreviation, a Name and a Description of the protocol, and may add custom fields to the protocol.

  • The Abbreviation needs to be unique and informative for all users. It must be no longer than 20 characters. This abbreviation will be offered for interpreting the data, and used as part of the description identifying the data. This is a required field.

  • The Name is an accurate name of the protocol. This is a required field.

  • The Description of the protocol is a free text entry that helps users understand the protocol as well as the limits on its use by the company. If there are multiple similar protocols, these descriptions will help users to decide which suits them better. This is a required field.

  • The Share With section lists all groups from Synergy that you are a member of. You have to select a group that will have access to the protocol, and become its owner group.

Procedure and procedure type deprecation

Use of procedure types (experimental, analytical, experimental-analytical) was deprecated in November 2019. Please download our template file example as a sample for regenerating your older template files.

Result type

To create a new result type, click the Add new button in the top right corner. To edit an existing result type, open the detailed view by clicking on it and click the Edit button. Modify the fields as needed and click the Save button. If you would not like to save the changes, click the X in the top right corner.

You need to provide an Abbreviation, a Name, an Aggregation Logic and a Description of the result type, and for numbers provide the Standard Unit, and the expected value range.

  • Different Data Type s can be selected: number, text or link. The fields to be filled in change as you select a new type.

  • The Name is an accurate long name of the result type. This is a required field.

  • The Abbreviation is a unique short description of the long accurate name. The limit is 20 characters. These abbreviations will be offered to users when uploading data, and used as parts of the titles in data viewing. This is a required field.

  • The Description of the result type is a free text entry that helps the user understand the result type. This is a required field. The limit is 4000 characters.

  • Variable checkbox: use this if your result types are variables of the experiment. This way, you can freely add information on your experiment parameters you inserted in the data table.

  • The AggregationLogic is the logic for aggregating the values of the result type. By default the data will not be aggregated. However, often there are multiple sets of processed data of a particular result type belonging to the same entity that must be aggregated. You can choose the following aggregation logics from a drop-down:

    • Arithmetic mean +/- Standard deviation (sample)

    • Minimum (provides the smallest numerical value of all of the aggregated items)

    • Maximum (provides the largest numerical value of all the aggregated items)

    • First (provides the value of the first item of all aggregated items that was populated into the database)

    • Last (provides the value of the last item of all aggregated items that was populated into the database)

  • The Standard Unit is a free text entry that defines the unit of the result type if it is a number. If it wasn't defined, Not set will be displayed. This is an optional field.

  • Set the expected range for the result types by setting a minimum value, a maximum value or both. You get a warning if the set minimum value is larger than the set maximum value. By default the number can range from - infinite to + infinite. Setting the minimum and maximum values are optional.

  • The number type has two options: scientific or decimal. Default setting is decimal, but working with very small or large numbers is easier with the scientific type.

  • The decimal places value is by default 2.

Tasks tab

The starting page of ChemAxon Assay lists current processed data upload tasks. The permissions to view and edit the processed data upload task in relation to its status is summarized in Table 1.

Status

Status marker

Viewing permission

Editing permission

Confirmed

images/download/thumbnails/1806198/status_confirmed_new.png

Anyone

None

Draft

images/download/thumbnails/1806198/status_draft_new.png

Anyone

Creator of the task, administrator

Aborted

images/download/thumbnails/1806198/status_abort_new.png

Anyone

None

Submitted

images/download/thumbnails/1806198/status_submitted_new.png

Administrator

Table 1. Status markers

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