Leeds construct management help

Rules which applies for recording the data

Prior to recording new data PiMS will try to find existing entry. If one is found, it will not create a duplicate record but link to the existing one. Therefore always try to stick to the same name for the same thing. For example if you used "Box 1" as a box name, next time when you recording something in the same box use this name. The system will create a new record for "Red Box 1" or "Box 11".
Other rules common for all constructs:

The name of the construct must be unique.
Position could have the following values - column A-P, row 1-24. For example the first position in the box would be A1 and the last P24.
For each location all information must be provided, i.e. Location and box and position in the box. Recording of partial locations it is not supported by the system.
"Saved By" field will be filled in with the name of the user logged into PiMS if the construct values are not loaded from PDF form.

All fields denoted by red start * are required.

Target and construct naming convention

If you follow the MPSI naming convention (which is that the target name starts with a 2 letter university prefix followed by 4 digits sequential target number) your constructs could be automatically associated with the target.

The construct name then, has to start with either "pMPSIL" or "pCR-MPSI" followed by 4 digit target number e.g. "pMPSIL0144" or "pCR-MPSIL0011" After the name which specified the target any text can follow. e.g. "pMPSIL0144 BL21 GOLD" If you want to (re-)associate the construct to another target you can edit the construct name, and the new target will be set.

Loading values from a PDF form

If you have a completed PDF form you can load values from it by clicking the link at the bottom of the page Load Entry Clone from PDF
You can load values from PDF forms for Entry Clone constructs, Deep-Frozen cultures and Primers. The page allows you to upload a PDF form with completed values.

Screen-shot 2.

Please note that you need Adobe Acrobat or similar software to edit the values in the forms.

Viewing Entry Clone Construct

Once you have recorded Entry Clone construct you will see a page where you can check the values saved and amend it if required. Points to note:

View target link appears at the bottom of the page ^*1
Primers have either inactive buttons or active buttons in line with their names. How it works
There are "List all" and Create new action links at the bottom of the page. More on "List all" you can find here
There is an "Edit" button at the bottom of the page
File management tab Detailed information
Deep-Frozen cultures tab Detailed information

Screen-shot 3.

Primers for Entry Clone or Expression constructs

Two primers which were used to obtain an Entry Clone can be recorded in PIMS. When recording an Entry Clone construct fill in Forward and Reverse primer fields with primers names. If the primers with the same name have been recorded in PIMS, then on a view Entry clone page view icon will be active. If clicked it will show view primer page. If icon is inactive there was no primer with such name recorded. You can record primers for Entry Clone any time later by recording a new Primer Form or by importing a primer order.

File management tab

Aims to provide file management capabilities for construct annotation.

Allows to add/remove files annotating the construct.^*2
Two files are specially annotated as Sequence and VNTI construct map files.
For any other files the description up to 250 characters long can be provided.
You can add any number of files, of any type.

Screen-shot 4.

Deep-Frozen cultures tab

This tab is for operation on Deep-Frozen culture stock. It allows to

Record new Deep-Frozen culture for this Entry Clone construct either by completing the form manually or by loading values from pre-comleted PDF form
View some details on the recorded Deep-Frozen cultures
View full Deep-Frozen culture

View Entry Clone construct Deep-Frozen cultures

Screen-shot 5.

Record Deep-Frozen culture for an Entry Clone construct

Please note that "Introduced plasmid" field is populated with Entry Clone construct name and it is not changeable.

Screen-shot 6.

Once Deep-Frozen culture has been recorded for an Entry Clone construct it appears on the "Deep-Frozen Cultures" tab. Please note that usual rules for recording of a new data will apply.

Screen-shot 7

Please note that more than one Deep-Frozen culture can be recorded for an Entry Clone construct.

Editing Entry Clone Construct

Some information can be amended after an Entry Clone construct is recorded. To do that click Edit button on a view Entry Clone construct screen.

Screen-shot 8 There are 3 types of fields on the page

Fields and information which cannot be changed. This type of fields is grade out e.g. Primers or Box bar-code.
Fields and information which can be changed from list of predefined options. These are drop-down lists e.g. Locations, boxes
Fields and information which can be freely amended. These are free text typing fields e.g. name, marker etc.

Required fields are denoted by a *. They cannot be left empty.
Other Tips & hits:

To associate the record to another target change a construct name so that it contains your target code. For more information about target and constructs name convention read this
Barcode is displayed for a current box only, and it is not changeable. To change a barcode for a box, plate or a clone saver card use Manage Boxes barcodes page.
Last location is a special location always represented by the card. Thus it is not changeable
Ambiguous input - When different locations are defined for the same box, the second location will take preference

Record Deep-Frozen cultures

You can record Deep-frozen culture for each individual Entry Clone construct. There is two ways of doing it.

You need to find the construct for which you are planning to record the culture and go to the "Deep-Frozen Culture" tab, and then click Record Deep-Frozen Culture link
From construct functions menu or menubar access Record new Deep-Frozen culture action

In the first case the Entry Clone name will be provided by the system, in the second you need to make sure that "Introduced plasmid" field name is populated with an Entry clone or an expression construct name which is recorded in PIMS. However, you can record Deep-Frozen culture even if there was no Entry clones or Expression construct recorded for it. Later you can add it and associate Deep-Frozen culture with later recorded Entry Clone or Expression construct. Please find how to do it here

Screen-shot 9.

Please note that usual rules for recording of a new data will apply.

View Deep-Frozen culture

Once Deep-Frozen culture is recorded it can be viewed. Please note the following:

Introduced plasmid field contains the name of an Entry clone or Expression construct.
In line with this field there is either inactive

or active button

If the button is active it will lead to view details of an Entry Clone or Expression construct record.

Files tab similar to the one described above for an Entry Clone
List all and Create new Deep-Frozen culture action links will list all recorded Deep-Frozen cultures and create a new Deep-Frozen culture correspondingly.

Screen-shot 10.

Edit Deep-Frozen culture

Some information can be amended after a Deep-Frozen culture is recorded. To amend the information recorded click Edit button on a view Deep-Frozen culture screen and make the changes.

Screen-shot 11.

Similar to edit Entry Clone page there are 3 types of fields on the page

Fields and information which cannot be changed. This type of fields is grade out e.g. Box bar-code.
Fields and information which can be changed from list of predefined options. These are drop-down lists e.g. Locations, boxes
Fields and information which can be freely amended. These are free text typing fields e.g. name, organism etc.

Required fields are denoted by a *. They cannot be left empty.
Other Tips & hits:

To associate Deep-Frozen culture to another Entry Clone or Expression construct while editing Deep-Frozen culture, choose appropriate construct from the list of constructs in the Introduced plasmid field.

To associate the record to another target change a construct name so that it contains your target code. For more information about target and constructs name convention read this
Barcode is displayed for a current box only, and it is not changeable. To change a barcode for a box, plate or a clone saver card use Boxes Barcode management page.
Ambiguous input - When different locations are defined for the same box, the second location will take preference

Barcoding

At the moment construct management functionality support barcodes for the first location (top on the construct form) box and position. Bar-code for box can be recorded in the creation time or added/change later. To change/add the barcode use Boxes Barcode management page. Barcode for the position can be changed by editing the construct.

List All Entry Clone constructs

List of all Entry Clone constructs recorded in the system could be obtained by clicking on List All Entry Clones in main construct menu or View All Entry Clones from the menu bar.

Screen-shot 12.

List is ordered by the name of the construct.
The following information is displayed.

Name
Designed by
Location (This is the first location of an Entry Clone sample)
Box (in the first location)
Position (in the first location)
VNTI map (VNTI map file. Displayed only if the construct was annotated with VNTI Map file)
Sequence (Construct sequence file. Displayed only if the construct was annotated with the sequence)

It is also possible to sort the list by "Designed by", "Location", "Box" and "Position. By clicking on the header of the columns of the table. Exporting options allows to export the information in the list to Excel, CSV, XML or PDF formats.

List All Expression constructs

List of all Expression constructs recorded in the system could be obtained by clicking on List All Expression constructs in main construct menu or View All Exp.constructs from the menu bar. The functionality is identical to the one offered by View All Entry Clone constructs with the difference that list shows only Expression constructs.

List All Deep-Frozen cultures

List of all Deep-Frozen cultures recorded in the system could be obtained by clicking on List All Deep-Frozen culture in main construct menu or View All D.Frozen cultures from the menu bar.

Screen-shot 12.

List is ordered by the name of the Deep-Frozen culture.
The following information is displayed.

Name
Designed by
Location (This is the first location of an Entry Clone sample)
Box (in the first location)
Position (in the first location)
Link to an Entry Clone or an Expression construct for which this Deep-Frozen culture was created (If no "Introduced plasmid" is set for a Deep-Frozen culture nothing will be displayed in this column)
VNTI map (VNTI map file. Displayed only if the construct was annotated with VNTI Map file)
Sequence (Construct sequence file. Displayed only if the construct was annotated with the sequence)

It is also possible to sort the list by "Designed by", "Location", "Box", "Entry Clone or Expression construct" and "Position. By clicking on the header of the columns of the table. Exporting options allows to export the information in the list to Excel, CSV, XML or PDF formats.

Notes

Note 1:
The link to the target appears only if the following conditions are satisfied

if the corresponding target has been recorded

Construct & target naming convention was followed

Note 2:
Files can only be deleted if the user has delete permission in PIMS.