note: before you start, please check that you have PiMS records for any Samples, Reagents, Targets and Constructs
  which you will refer to in your plate experiment.

Mouse over "Experiment" in the menu bar, and select New Plate Experiment.
You will see a 'Create plate Experiment' form with 4 tabs: 'Basic details', 'Quick setup', 'Plate view' and 'Spreadsheet view'.
Only the 'Basic details' tab is accessible.

Basic details

Mandatory details:

• Enter a name for the plate, e.g. the bar code or label you will find it by later.
  
  
• Choose the type of the plate from the drop down list.
   note: If an appropriate type is not available in the list, please speak to your PiMS administrator.
  
  
• Choose the PiMS "protocol" for the experiment.
  This acts like a template, setting the details which you can specify for your experiment.
  
  
• Select the "Start" and "End" dates. By default, these are set to the current date.
  To select a different date, either edit the default value, or click the calendar icon and select a new date.
  
  
  

Optional details:

• Enter any additional information in the details field.
  
  

When you have finished, click on the button at the end of the form.
The details of the plate experiment will be displayed.

  note: It is also possible to populate the details for a Plate Experiment by uploading a spreadsheet containing the data.
  -see Uploading data from a spreadsheet.

This is the first tab you will see after you have entered the details of your plate and chosen a protocol.

All the Input samples specified in your chosen protocol are listed here, followed by all the Parameter definitions.
Any default values in the protocol are already filled in.

In this example a 'Dish culture' protocol has been selected, which has 1 input sample -"Cells" and 4 Parameter definitions.
The default Parameter values for 3 of these 'Colony size', 'Growth conditions' and 'Plate type' are filled in, but are editable.

Specifying samples

For every sample listed in the protocol, you will see the following:

• A 'sample' icon and the role the sample plays in the experiment.   -in the example this is 'Cells'.
  
  
• A box labelled 'Volume:' -to enter the amount of the sample (in microlitres).
  
  
• The name of the 'Sample:'
  If no default sample is set, this will say "(None)" -as in the example.   -see Choosing samples below.
  
  
• The checkboxes, to the left of 'Volume:' and 'Sample:' are used to set the specified values for the whole plate.
  
  • To add the same Volume of a Sample to each well, check both the 'Sample' and the 'Volume' boxes.
      -as in the example
  • To add the same Volume of a different Sample to each well, just check the 'Volume' box.
      -you can specify the individual samples in the Plate or Spreadsheet view.
  • To add the same sample to all wells, but vary the Volume (for example, when setting up a gradient),
    just check the 'Sample' box.
  • If none of the above is true, you do not need to specify either in Quick Setup.
    -leave both boxes unchecked you can specify the volume and sample values for individual wells in the Plate or Spreadsheet view.
    
    

Choosing samples

To choose a sample, click on the name of the sample. A popup, displaying a list of all 'Sample' records in PiMS, will appear.

• In the popup either, scroll down the list to find the correct record in PiMS.
  
  
• Or, to refine the list, enter a term(s) in the search box(es) and click the button.
  
  
• Click the "Select" link next to the correct sample.
  The popup will close, and the name of the sample will change to match your selection.
  
  
• If there is no matching sample record, you will need to close the pop-up window and leave the Plate view.
  To create a Sample record, select 'Create New Sample' from the Sample & Reagent menu. You can then continue recording the details for your plate experiment. -see Locate a Plate experiment record.

Specifying Parameter values

In the 'Quick setup' tab, a list of all 'Parameter definitions' in the selected protocol is shown -below the list of samples.
All are displayed in the following format:

• The name of the Parameter definition -in the example this is 'Number of colonies'.
  
  
• A symbol -which shows what kind of information is needed:
  for text
  for numbers   -as in the example
  for true/false
  
  Text and number values have a box into which you can type the value you want to set. If the protocol has a default value, this will be shown in the box.
  Numbers may be restricted to whole number values only, or have a minimum and/or maximum value.
  These restrictions are shown next to the box.
  True/false values are represented by a checkbox, with the Parameter definition name beside it. The box will be checked if the default value is "true", otherwise it will be unchecked.
  
  
• As for Samples, the checkbox to the left of the Parameter definition name, is used to set the specified value for the whole plate.
  If the checkbox to the left is cleared, the value will not be set.
  For text and number values, the box will be greyed out.
  

Saving the values

Review the values you have specified, and verify that any details to be ignored have their corresponding checkbox unchecked. When you are satisfied that everything is correct, click the button at the bottom of the page. PIMS will set the values you have given, for each well in the plate. You will then see the Quick Setup view again.

Click on the "Plate view" tab to see the plate view.

As for Quick Setup, all the Samples and Parameter definitions are listed on the left-hand side.
If a Sample or Parameter definition has a value set for all the wells in the plate, there will be a beside its name.
-in the example, the Sampe called 'Cells' has been set.

To the right is a representation of the plate. The selected wells are highlighted in blue.
-in the example, well 'A1' is selected.

To make changes using the plate view, first select a range of wells to which the changes will apply, then specify the sample or parameter value(s) and save.

Selecting a range of wells

• To select a single well, click on it.
  
  
• To select a rectangular block of wells, put the mouse cursor over one well, hold down the left mouse button, and move the cursor to another well.
  You will see the selection change as the cursor moves across the plate.
  Release the mouse button when you have selected the correct range of wells.
  
  
• There are some short-cuts, which make certain selections easier. Click the appropriate icon to make the selection:
  selects all wells
  selects the adjacent row
  selects the column below
  
  Clicking on a row or column label (A-H or 1-12) will also select the appropriate row or column.

Specifying parameter and sample values

Click on the name of the Parameter definition or sample. This will open up a form directly below
-in the example, a Parameter definition called 'Colony size' is shown.

• Enter the value that you want to set, or edit any default value as necessary.
    -in the example, a default value of 2mm is already specified from the protocol (experiment template).
    -If you need help with this, please refer to Specifying samples or Specifying Parameter values in the Quick Setup help section.
  
  
• Click . PIMS will save the Parameter or Sample value you set, for each of the selected wells on the plate.
  
  note: You can only change the value for one Parameter definition or sample at a time in Plate view.
  The button next to the value will save that value only.

Viewing existing values for a well

Tooltips

To see a recorded Parameter value, hold the mouse cursor over the well you are interested in and read the tooltip:

The tooltip lists all the Parameter definitions and samples, for the selected well, along with any values which have been set. Where a value has not been set the tooltip displays "Not set" in red. The details for a sample or Parameter definition, selected in the lhs panel is displayed in bold.

In the example, the tool tip for well 'A1' of the 'Plate example' is shown.

This indicates that:

• The values for Volume (50µL) and Sample name (My transformed cells) for the Sample called 'Cells:', have been specified.
• The Parameter values for 'Colony size:' (3mm) and 'Number of isolated colonies:' (25) have also been specified.
  
• The Parameter value 'Plate type:' has not been specified.
• The Parameter value 'Growth conditions:' has been specified, using the default value from the protocol.
    -this Parameter definition is selected in the lhs panel and is displayed in bold in the tooltip
    -the 'text' symbol is displayed in the selected well, indicating that its value has been set.

Plate icons

For a more general view of a particular Sample or Parameter definition, in the entire plate, click its name in the lhs panel.
(An edit form will open underneath it - this can be ignored.)

In the plate, any wells with a value set for a selected Parameter definition will have the appropriate symbol in them:
for text
for numbers   -as in the example
for true/false

For a selected Sample, a well containing a flask icon means that values for both the sample name and the volume have been set. If only one value has been set, you will see instead.

In the example, the Sample called 'Cells' has been selected in the lhs panel.

• Both the volume and sample name have been set for the well A1 -as indicated by the .
• By contrast, one or both of these values has not been set for all other wells in the plate.
    -the tooltip, displays the Parameter definitions and samples for well A2 and shows: Cells: 150uL Unspecified
    indicating that only the volume has been specified, hence the icon in the well.

Plate overview

At the top of the list of Samples and Parameter definitions, you will see "Plate overview". This works in a similar way. On clicking this label, any wells with a value for all Parameter definitions, and both a volume and a sample name for all samples, will be marked with a .

In the example, the tooltip for well G11 indicates that all Sample and Parameter values have been specified.

Click on the "Spreadsheet view" tab to see the spreadsheet.
Use this tab to enter and update values for the individual wells in a spreadsheet format.

The spreadsheet is a tabular view of all the Parameter values and Samples in the plate. There is one column for each Parameter definition in the protocol, and two columns for each Sample: sample name, and sample volume.
Each well in the plate is represented by a single row in the spreadsheet. Use the scroll bar at the rhs of the spreadsheet to locate the row for a specific well.
To see all the details recorded for an experiment in an individual well, click the icon in the first column. You will see a PiMS 'Simple' experiment view with the details in five tabs.
  see View and update Experiment details.

Changing values

Status: (experiment status)
  Select the Status 'To be run', 'In process', 'OK' or 'Failed' from the drop-down list.

Output: (Output sample)
Click the Output sample name to see the details (View) page for the output sample.
  -see View page for a Sample for more details.

Text and number parameters, and sample volumes:
  Click in the relevant table cell. You can then delete any existing value and type a new one.

True/false parameters:
  Click the checkbox in the relevant table cell to tick or clear it.

Samples: (Input samples)
  Click on the name of the sample - if no default sample is set, this will say "(None)".
  A popup will appear, in which you can search for the correct sample.
  In the popup, click the "Select" link next to the sample.
  The popup will close, and the name of the sample will change to match your selection.
  (For more help on this, see Choosing samples.)

Saving values

Click the button at the bottom of the tab.

It is also possible to populate the details for a Plate Experiment by uploading a spreadsheet containing the data.
First, complete the mandatory details in the Basic details tab:
  -enter a name or barcode for the plate, select a plate type, a protocol (template) and the start and end dates for the experiment.

Click the button and navigate to the spreadsheet on your computer, then click the button.
The details of the plate experiment will be displayed in the tabbed views.

Spreadsheet details:

To locate a Plate experiment record either:

• Select 'View All Plate Experiments' from the Experiments menu
    or
• Click 'View all Holders' link in the 'Holders' section in the People & Places Functions page
    or
• Click the 'Search Holders' link in the People & Places Functions page, then enter the appropriate term(s) in the search box(es)
    or
• Click the 'Access by Barcode' link from the PiMS home page or the Experiment Functions page, and enter the barcode or name used to identify the plate.
  
  

To view and/or update the details click the icon next to the appropriate experiment in the list.
You will see the Plate experiment details with the 'Quick setup' tab open.
  -see Quick setup

You can link PiMS Plate Experiments to match the sequence of Plate experiments you might perform in the lab.
In order to do this, you need to create 'Protocols' (experiment templates) where the 'specification' or 'Type' for the Output sample from the first Experiment protocol will match that of an Input sample for the next Experiment protocol.
  -see Output and Intput Samples for more details.
Where possible, PiMS will suggest possible 'Next' Experiment types based on the sample 'Type'.

To 'Create' the Next Plate Experiment:

• Open a Plate Experiment record and click the 'Basic details' tab.
  
  

Under the section headed:

Perform new experiment with these samples:

You will see a list of possible 'Next' experiments represented by:
 Role, for the samples as experiment Input Samples, defined by a Protocol (experiment template).
  -in the example, the sample could be used as an Input sample called 'Insert' in a 'LIC polymerase reaction'

• Click to see the the 'Basic details' tab for a new Plate experiment with the Protocol field populated
  
  

There is also a link to the 'specification' for the sample which joins the Plate experiments together, and a link to the Plate experiment where it was created.
  in the example this is shown as:   Loading Insert from the plate: Plate Example

• Complete the Basic details, and click
  
  
• You can then record and update the details for the new experiment.
   note: The relevant sample details will be completed.
   also: Any Target or Construct, which was defined in the first plate experiment, will also be defined for the wells of the new plate.
  
  

You can also use the Output sample from an individual well of the plate as the Input sample for a new experiment.

• Click the spreadsheet tab
• Click the 'Output' link in appropriate row of the plate
• From the resulting Sample View page, select the Experiment type from the list under the heading:

  Perform new experiment with this sample:

    -see Linking Experiments