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PIMS Leeds Primer management help
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Table of contents

Primers actions

To use these functions, switch to the "Leeds" perspective.
Primer functions
Screen-shot 1.

Record New primers

At the moment PIMS supports recording of the primers only in pairs. Thus, the primer form contains two primers, one Forward and one Reverse Primer. In addition to them there is some common information for both of them.
New Primers
Screen-shot 2. (Only shows Forward primer, but reverse looks exactly the same)

All fields denoted by red start * are required.

New Primers details
Screen-shot 3. (Shows primer common details, appears together with forward and reverse primer which is shown above)

Grayed out fields calculated automatically thus, cannot be filled in.
Common rules applies.

Please also note that the primers to be successfully linked with the constructs need to have the same name as the ones which were used when the construct was created.
However, the order of creation is not important. You can either first create Entry Clone construct and specify not-yet-recorded primer's names. Then, create primers with the same name. The link from the construct to the primers will appear automatically.
Alternatively if the primers names were created first (either from loading a batch order or recording individual pair of primers), and then the construct, the link between them will be established automatically.

The system will prompt you if there is an inappropriate data in the field.

Load primers from PDF form

Values for the primers can be loaded from pre-completed PDF form.
Load from PDF
Screen-shot 4.
Primers which have been recorded individually can be updated by loading the batch order. If the batch has the primer with the same name and the sequence. The system instead of creating a new primer will try to add missed details to already recorded primer. The following rules will apply:
  • If Invitrogen order is loaded no details is added
  • If custom Leeds order is loaded the following is added
    • Optical density OD
    • Primer's Molecular mass
    • Amount of the primer in a sample (ng)
  • Details can only be added, no information which is already recorded can be overridden
However, this will not work other way around. For example is the primers were first recorded by loading the primer order. The system will not allow to record the primer with the same name once again. Please note that you can amend the details of the primers as described in Editing the primers

View Primers

Primers can be found in the system using List all primers Once found the system will display them as shown below
View Primer
Screen-shot 5. (Only one primer shown, Reverse primer is likely to contain another details)
View Primer Details
Screen-shot 6. (Primers details, shown together with the primers)

There is also self explanatory links to "List all" and "Create new" primers actions at the bottom of a page and "Edit" button which will forward you to Edit primers page

Edit Primers

Edit primers page allows to amend the details of the primers previously recorded.
Edit primers
Screen-shot 7. (Please note only one primer is shown)
Edit primers details
Screen-shot 8. (details are displayed together with the primers)

Please note that some fields are not changeable. These are calculated fields.
Please use separate box barcode management page to change the value of barcode for a box.
The value of the current box barcode is displayed in the non changeable barcode field.

Constructs and Primers

There is a link between primers and construct. In particular "Plasmid concerned" field displays the construct which was obtained using these primers.
Construct primer link
Screen-shot 9.

This field is changeable and by choosing the construct from the list you can specify which construct was obtained using these primers.
For simplified navigation the values in the list grouped in 3 categories.

  • Not recorded
  • Entry Clones
  • Expression constructs
The first group may not appear in case if current construct was recorded in PIMS. If appears it will always contains one element only current value of "Plasmid concerned" field.
The second group lists the names of all Entry Clone constructs recored in the system.
The third group lists the names of all Expression constructs recored in the system.
This list is accessible from Edit Primers page.

At the same time there is a button from the Entry Clone or Expression construct to view the details of a primer.

View Primers Icon
Screen-shot 10.
When either of the buttons inline with primer names is clicked the view single primer page will be displayed.
View Single primer
Screen-shot 11. (View single primer page)

There is two additional links on this page.
One View Cloning design experiment will forward you to View primers page.
Second will lead to the file management page, which allows you to add/delete files which annotates the primer. (Those files are either loaded from Order batch or added manually).

List all primers

List all primers display the following information on the primers.
  • Forward / Reverse Primer names
  • Designed by
  • Location
  • Box
  • Forward / Reverse primers positions
  • PCR product length
  • Plasmid which was obtained with these primers
List all Primers
Screen-shot 12.

Information sorted by Forward / Reverse primer names, but can be reordered by any other displayed values. Export options available - Excel, PDF, CSV, XML.
Hit & tips

  • Plasmid concerned link is not active if the plasmid with specified name is not recorded (once the plasmid with that name is recorded, the link will become active and lead to view this construct page)

Some primers displayed on the screen-short 12 come from batch order. (Primers with box called "Plate (from order) 24500") Whereas other information come from individually recorded primers. Primers recorded from Invitrogen batch order and custom Leeds batch order will also contain different subset of information. Please find more about it on the Record primer order help pages
PIMS for MPSI
Version 3.0