Details of the PiMS functions relating to Targets can be view on the " Target Functions" page.
This is reached by clicking "Target" in the horizontal menu bar near the top of each page in PIMS, or by selecting "Target Functions" from the Target drop-down menu.

This page contains links to the functions which are also listed in the Target menu:
Search Targets, New Target, Download Target, New DNA Target, Search Complexes, New Complex, Search Target Groups, Search Projects, Similarity Search, Scoreboard, Reports.

In addition there are links to Search for Molecules (DNA and Protein), Database references and relevant Reference data such as Organisms (Species or Natural source), Target statuses and Database names.

To locate a PiMS Target record you can either:

• select the Target from the list displayed when you click "Targets" in the breadcrumb trail at the top of Target details page
  -see Target list
• select the Target from the list of "Targets found" which is displayed when you select "Search Targets" from the Target menu or click the "Search" link in the Target Functions page
• or, if you have recently viewed the Target record, select it from your History list -see History help

Target List

To see a list of all Targets currently recorded in PiMS, navigate to a target details page and click "Targets" in the 'breadcrumb' locator at the top of the page. -see Target details
A list of Targets is also displayed when you select "Search Targets" from the Target drop-down menu or click the link in the 'Target' section of the Target Functions page.
You will see a page similar to the one below which states the number of Targets recorded in PiMS.

• Click

  Targets :

  to display a list of all Targets recorded in PiMS. -see Target List
  
  
• Click Workflow to see a graphical representation of the target and its use.   -see Target Diagram
  
  
• If you have permission to delete the Target record you will see a green delete icon and link Delete
    this is not the case in the example where Can't delete is shown
  
  
• In open box labelled 'Target Details', click the context menu link next the the Organism name
  -Bacillus anthracis in the example
  You will see links to both the PiMS record for the organism and the NCBI taxonomy record.
  
  
• To edit the Target details click Make Changes... -this will not be visible if you do not have permission to edit the Target details.
  You will see the editable version of the target details box.
  
  
  When you have finished editing, click the button or click (Cancel editing) to revert any changes you have made.
  
  

To examine the contents of each box, click the plus icon.


Seqences contains the DNA and Protein sequences for the Target.
For each sequence there is also a pop-up link to display the Fasta-formatted sequence in a pop-up window.


You may edit the Target sequences by clicking Make Changes... in the box.
  -note: if your Target lacks either a DNA or Protein sequence, PiMS will allow you to add the missing sequence.

Add a missing Sequence to a Target

If your target lacks a DNA sequence the 'Sequences'box will display a button.

1. Click the button
2. Click Make Changes...
3. Paste the DNA sequence into the box labelled 'DNA sequence'
4. Click
   
   

If your Target lacks a Protein sequence follow steps 2-4 above.


Constructs contains a list detailing the Construct records for the target.
The list includes links to Experiments recorded for each Contruct and the latest "Milestone" which has been achieved.
In PiMS a Milestone can be set when the success of certain Experiments are recorded. When a Milestone is achieved the Target is progressed along the protein production pipeline. Target Milestones relate to the "Status" of a Target defined in TargeDB.
  -the example list contains one construct 'BACAN_GLMS.con1' which has achieved the milestone 'PCR'

  note: If the Target has no Construct records, you will see 'No constructs found!' in place of the list


Experiments contains a list of Experiment records for the target.


The details displayed for each Experiment can include:
  Milestone -a link to the Target Milestone record if one has been achieved -see New Milestone
  Experiment -a link to the PiMS Experiment record -see Experiments help
  Type of Experiment -a link to the description of PiMS experiment type, if known
  Experiment Date -the date the Experiment was recorded in PiMS
  Protocol Used -a link to the details of the PiMS protocol (Experiment template) used
  Experiment Status -this can be 'To be run', 'In process', 'OK' or 'Failed'

  note: if there are no Experiments recorded for the Target, you will see 'There are no experiments on this Target' in the Experiments box

To record a new Experiment for the Target, click the New Experiement link in the box header.
  -for help see New Experiment



Database references contains a list detailing records in remote databases for the target.
In the example the list contains the details for 1 record.

The details displayed for each Database reference can include:
  Database -the name of remote database -if known
  Accession -the unique identifier for the record in the remote database, provides a link to the actual record
  Type -the type of record, e.g. sequence, literature reference etc.
  Sequence release -the release number of the database

In the example, the GenBank record was created from the GI number entered when the Target was recorded.
Click the 73919642 link to see the NCBI report page for the Target protein.


Blast searches contains links labelled 'PDB Blast results' or 'TargetDB Blast results'.
Clicking these initiates Blast searches for the target protein sequence against the PDB or TagetDB respectively.
  -see PiMS Blast searches for more details

Images, Attachments and Notes

Boxes labelled "Images", "Attachments" and "Notes" are found on most PiMS view pages.

Attachments allows you to link Files with the Target.
To make a link from the target to a file on your network, open the Attachments box, then click the button and navigate to the appropriate file. Enter a description for the file then click

The box will be re-displayed with a link to the uploaded file (called Target data.doc in the example below).

You can update the file details by clicking Make Changes...

You may also delete the file by clicking the green delete icon.

If you do not have permission to edit the Target, you will not be able to make a link to a file.
You will see e.g. 'You do not have access rights to attach files to 000002' in place of the Browse button.

Images allows you to associate images with the Target.
This is similar to Attachments but you can also record a title and legend for the image.
These are displayed in a table with a clickable thumbnail to the original image.

Notes can be used to keep a record of changes to a Target in PiMS. A note contain the date it was recorded by whom (the default is the id of the person currently logged in) and a short description.
A default note is updated each time the Target is viewed, with the date and time, but this is not saved automatically.

The example shows a note dated 03/12/08 and the default note.

Information about the Primers is displayed in the top part of the Construct Details table.
The complete sequence of the Forward and Reverse Primers and also the gene-specific or 'overlap' sequence and any 5'-extension is displayed. The length, Tm °C and %GC for both the complete and overlap sequence are also included.

The sequence of the predicted PCR sequence is also displayed along with the calculated size and %GC residues.

  note: -these details are not editable

• The complete sequence of the Forward or Reverse primers can also be displayed in Fasta format by clicking the Fasta pop-up link.
    -the sequence will be displayed in a pop-up window
  
  

Information about the Construct Protein (Expression product) is displayed in the bottom part of the table:

• You may edit the details in the table which have a white background. Then click (at the bottom of the table).
  If you do not have permission to edit the Construct, all fields will have a blue background and the 'Save' button will not be visible.
  
  
• To see a complete Construct Protein sequence, click the relevant Fasta pop-up link.
    -the sequence will be displayed in a pop-up window
  
  
• To see a table detailing all Experiments performed using the Construct: click All Experiments   -see Construct Experiments
  
  
• To record a new Experiment using the Construct: click Add New Experiment   -see New Result
  
  

• To view the details of an Experiment, click on the appropriate link in the Experiment column.
  This will display a PiMS 'Simple' Experiment view.   -for help see PiMS Experiment Details.
  
  
• Click Record New Experiment to record a new Experiment using the Construct.   -for help see Recording a PiMS Experiment.
  
  
• Construct Experiments are also represented graphically in PiMS
    -see Construct Experiments diagram

PiMS provides a visual representation of Targets and Constructs and their use -the Diagram View.
This can be accessed from the 'Workflow' link on a Target or Construct details page.
The Diagram view provides a simple form of navigation between Target, Construct and Experiment records in PiMS.

Research Objective
For each new Target recorded in PIMS, a "Research Objective" with a single "Research Objective element" is automatically created.
A Research Objective defines what you are planning to work on.
This might be a Target, or combination of Targets, Target-domains and /or other molecules, where each of these is a Research Objective element.

So, in the case of a new Target, a new Research Objective record is created using the Target's Protein name as an identifier. The Target itself is a default Research Objective element representing the 'Full length' sequence, within this Research Objective.  Similarly, when you create a new Construct record, another new Research Objective record is created using the Construct's name as an identifier. In this case the construct is a Research Objective element representing the protein you intend to express.

When you record the details for an experiment in PIMS, the experiment is linked to the Target via the an Research Objective.   -see glossary entry for more details.

Target Diagram

Targets, Research Objectives, Research Objective elements and Experiments are represented by different shaped symbols linked by arrows. A brief description of the specific items in a diagram can be seen in a tooltip when you mouse-over the symbol.

The example shows the result of clicking the 'Workflow' link from the target details page for Target BACAN_GLMS.

• The Target is represented by an irregular pentagon with a red border labelled: 'Target', followed by the Target's 'Name' -000914 in the example.
    -click this symbol to return to the Target details page.
  
  
• Research Objective elements are represented by blue octagons labelled with the start and end residues in the Target sequence which define the expressed protein.
  -'Default' for the Full length Target and 'Res 2-599' for the Construct in the example
  
  
• Research Objectives are represented by blue diamonds labelled with either a Target's 'Protein name' or a Construct name.
  -'000914' for the Target and 'BACAN_GLMS.con1' for the construct in the example
    -click this symbol to see the relevant Target or Construct details page.
  
  
• Experiments which have achieved a Milestone are represented by blue ellipses labelled with the name of the Experiment.
  -the example shows that 2 of the Experiments performed using Construct BACAN_GLMS.con1 have achieved Milestones, these are also listed in the Construct Experiments table and the Experiments box for the Target.
    -click this symbol to see the full details for the Experiment. -see View Experiment details.
  
  

Construct Diagram

This is a subset of the Target diagram only showing symbols which are relevant to teh particualr Construct.

Construct Experiments diagram

The Blue ellipse represents the Construct Design Experiment, which is recorded automatically when you create a new Construct.
Clicking the ellipse will open an Experiment view page displaying the full details. -see View Experiment details.

The 3 trapezia are links to the three 'Output Samples' from the Experiment:
Template: Construct nameT, Forward primer: Construct nameF and Reverse primer: Construct nameR.

Each time you record a new Experiment for the Construct, an extra ellipse will be added to the diagram, labelled with the name of the Experiment.