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PIMS SRS > Use Case Suite > Sample Tracking Use Cases

Release Information

Project: PIMS
Internal Release Number: 0.1
Related Documents:

Default Aspects of All Use Cases

Direct Actors:
User: end-user in any role
System: The PIMS system being built
Admin: Web-site administrator, has authority to perform security-critical operations.
Scientist: Post-graduate or post-doctoral wet lab scientist
Senior Scientist: Post-doctoral scientist
Group leader: someone with authority to add users to a group, usually a senior scientist.
Technician: Technical staff
Experimenter: Scientist, or technician sometimes PI
PI: head of lab
When actors are not listed, assume User is doing it.
Items beginning with "see" indicate that System has presented a new screen.
Stakeholders: Project Owners and other members
Prereq: User is logged in except for UC-Log in
TIP: See detailed tips in the guidelines for writing use cases.

Use cases


Target management
UC-Add new target
UC-Edit target
UC-View target status
UC-Add details of a citation to a target
UC-Find citations relating to a target

Bioinformatics
UC-Target selection
UC-BLAST sequence
UC-Genomic DNA available
UC-cDNA available
UC-Is target registered
UC-Align sequences
UC-Predict TM helices
UC-Design primers
UC-Order primers

Sample Tracking
UC-Create sample
UC-Edit sample
UC-Track sample
UC-Sample discard
UC-Move sample
UC-Generate barcode
UC-Scan barcode
UC-View current experiment outputs
UC-View location

Reagent management
UC-Add reagent
UC-Edit reagent
UC-New container
UC-View reagents

Experiment/Protocol management
UC-Create protocol
UC-Edit protocol
UC-View protocol
UC-New experiment
UC-Update experiment
UC-Add next experiment
UC-Remove experiment
UC-Create screening solutions
UC-New crystalization plate
UC-View experiment
UC-New multi-well experiment
UC-Screen conditions

Project management
UC-Create project
UC-Add target to project
UC-Add user to project

Logging in and out
UC-Log in
UC-Log out

User account management
UC-Reg new user
UC-New passwd
UC-Edit profile
UC-View profile

Data Access Rights management
UC-new-owner
UC-new-group
UC-add-user
UC-remove-user
UC-add-permission
UC-remove-permission
UC-add-create
UC-remove-create
UC-new-condition
UC-set-condition

Reporting
UC-Print protocol
UC-Print experiment
UC-Audit trail

Interfacing to laboratory instruments
UC-Robot-input
UC-Robot-input-series
UC-Robot-control
UC-Robot-generate
UC-Robot-convert

Data mining and visualisation
UC-Search PIMS

Installation and upgrading
UC-Config site
UC-Submit form

Mobile data collection


Workflow tools


Scheduling

UC-Create sample: Create a new sample

Summary: An experimenter will often need to create a new sample which describes either the input or output components of an experiment.
Will require details of the individual sample components, the holder, container and location. The component details may already be recorded in PIMS as reagents.
A new sample might also be created on receipt of a delivery of a laboratory reagent(s).
Importance: Expected
Priority: Expected
Use Frequency: Often
Direct Actors: Experimenter
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. visit "SAMPLE" page
  2. click to create a new sample
  3. see "new sample entry" page
  4. enter sample name or identifier and other details as required
  5. select holder and/or container and location
  6. define sample component(s) from pick-lists and enter concentration
  7. perform UC-Submit form: Submit information in a form
Alternative 2a
Scenario Extensions:
    A new sample has been delivered to the laboratory
    1. click to "import" new sample
    2. see "REAGENTS" page or menu
    3. perform UC-Add reagent: Add a new reagent to PIMS steps 2-10
    4. perform UC-Create sample: Create a new sample steps 3-7
Alternative 2b
Scenario Extensions:
    A new sample has been transferred from a collaborating laboratory
    1. click to "move" sample
    2. perform UC-Move sample: Move a sample between labs steps TO BE DETERMINED
Alternative 4a
Scenario Extensions:
    Sample (or components) or holder is barcoded
    1. perform UC-Scan barcode: Scan a barcode Alternative 1a steps 2-5
Alternative 5a
Scenario Extensions:
    Container does not exist in PIMS
    1. select option to "add new" container
    2. perform UC-New container: Add a new container to PIMS steps TO BE DETERMINED
    3. perform UC-Create sample: Create a new sample steps 6-7
Alternative 6a
Scenario Extensions:
    Sample component details do not exist in PIMS
    1. select option to "add new"
    2. perform UC-Add reagent: Add a new reagent to PIMS steps 3-10
    3. perform UC-Create sample: Create a new sample steps 6-7
Alternative 7a
Scenario Extensions:
    Details are incorrect
    1. click to edit sample details
    2. perform Edit sample: Edit sample details steps 3-6
Notes and Questions
  • will require sample component details (and holders, locations and containers) to be selectable from lists.
  • where new sample is a delivery, system will need to update Experiment.ImportSample table. This will include crystalization screens and primers delivered in multi-well plates.
    System will also ned to link user back to new sample entry page
  • Can we prevent users creating multiple samples with the same name?

UC-Edit sample: Edit sample details

Summary: An experimenter may need edit or update the details for a particular sample. This will be required if the details entered initially were incorrect or incomplete. Also if a new sample is to be created from an existing sample. Will also allow a user to view the current location and other details of a sample
Importance: Expected
Priority: Expected
Use Frequency: Sometimes
Direct Actors: Experimenter
Prereq:
User must belong to a user group with appropriate access rights
The sample exists in PIMS
Main Success Scenario:
  1. visit "SAMPLE" page
  2. click to select sample to edit
  3. see sample's view page
  4. edit appropriate fields
  5. perform UC-Submit form: Submit information in a form
  6. system logs record of changes made including user Id, date and details
Variations
  1. a new sample can be created from an existing one by selecting this option
Notes and Questions
  • will require option to "save as"

UC-Track sample use: Track sample use in PIMS

Summary: A user may wish to monitor the use of a sample, reagent, plasticware etc. in PIMS.
Importance: Expected
Priority: Expected
Use Frequency: Often
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. perform UC-Search PIMS Search data held in PIMS steps 1-3, entering or selecting appropriate details to identify the "sample".
  2. see information retrieved from PIMS for all records relating to the selected "sample"
Alternative 1a
Scenario Extensions:
    "Sample" has barcode
    1. perform UC-Search PIMS Search data held in PIMS Alternative 3a
    2. see information retrieved from PIMS for all records relating to the selected "sample"
Variations
  1. sample details might include a unique identifier, or be less specific such as a type of sample, reagent or plasticware
Notes and Questions
  • may overlap with UC-View target status in some instances
  • selectable search criteria will enable a user to narrow a search
  • results should be displayed with clickable links to the relevant view page(s)

UC-Sample discard: Discard a sample

Summary: An experimenter informs PIMS that a sample has been discarded.
Importance: Expected
Priority: Desired
Use Frequency: Often
Direct Actors: Experimenter
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. visit "SAMPLE" page
  2. click to select the sample to view
  3. see the sample's individual view page
  4. click button to discard sample
  5. system displays request to confirm sample to discard
  6. perform UC-Submit form: Submit information in a form steps 3-5
  7. system clears sample location, sets amount to zero and logs record of changes made including user Id, date and details
Alternative 1a
Scenario Extensions:
Alternative 5a
Scenario Extensions:
    Incorrect sample discarded
    1. click button to retrieve sample
    2. perform UC-Sample discard steps 5-6 but confirming retieval
Variations
  1. same steps are used where a reagent, holder or container is dicarded, but need to visit appropriate page initially
Notes and Questions
  • will require all samples (and holders and containers) to be selectable from a limited number of pages
  • Will need discard and retrieve options

UC-Generate barcode: Generate a barcode

Summary: A user may wish to instruct PIMS to create unique barcodes to facilitate the tracking of samples, reagents and consumables.
Sheets of adhesive barcode labels will be printed which can be affixed to solid surfaces such as sample containers
Importance: Desired
Priority: Desired
Use Frequency: Often
Prereq:
User must belong to a user group with appropriate access rights
Direct Actors: System, Experimenter
Main Success Scenario:
  1. visit relevant area of PIMS (TO BE DETERMINED)
  2. user instructs PIMS to generate new barcode(s)
  3. system creates new barcode(s) and stores information
  4. user instructs PIMS to print label(s)
  5. system prints label(s)
Alternative 1a
Scenario Extensions:
    Barcode generator is not part of PIMS system
    1. TODO

UC-Scan barcode: Scan a barcode

Summary: To assist with sample tracking, and to minimize data-entry errors, a user may wish scan a "unique" barcode which is physically attached to samples.
PIMS will then associate the barcode with stored information relating to the selected sample or reagent.
NOTE: Samples and reagents may be delivered to the laboratory with a supplier's barcode attached. Where this barcode is a "unique" identifier, the barcode may be used in PIMS. Alternatively, where the barcode is the supplier's product code, a PIMS-generated unique barcode should be used in preference.
Importance: Expected
Priority: Desired
Use Frequency: Often
Direct Actors: System, Experimenter, Barcode reader
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. user scans barcode with hand-held device
  2. system displays information associated with the barcode as appropriate view page
Alternative 1a
Scenario Extensions:
    User wishes to use barcode for entering associated information in a data-entry form
    1. visit appropriate data entry page
    2. click in "code" field
    3. scan barcode with hand-held device
    4. system inserts barcode information
    5. system records association with barcoded sample when form is submitted
Alternative 2a
Scenario Extensions:
    Barcode not currently recorded in PIMS
    1. see message indicating barcode not recognized
    2. click to cancel
    3. perform UC-Scan barcode: Scan a barcode Alternative 1a steps 1-4
    4. enter additional information -as appropriate
Variations
  1. Samples, reagents and other laboratory consumables (e.g. plasticware) can be barcoded
Notes and Questions
  • How can we resolve conflict where a supplier's barcode is already used in PIMS

UC-Move sample: Move a sample between labs

Summary: Samples may be moved between collaborating laboratories with different expertise in parts of the protein production and crystallization process
Importance: Expected
Priority: Expected
Use Frequency: Sometimes
Direct Actors: Admin, PI, Senior scientist
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. user informs PIMS that a "sample" has been moved to or from an external laboratory
  2. TO BE COMPLETED
Alternative 1a
Scenario Extensions:
    Laboratories share access to the same PIMS installation
    1. perform UC-Edit sample: Edit sample details, entering new location at step 4
Notes and Questions
  • will need protocol for collecting all information relating to the "sample" in the donor PIMS and exporting it to the recipient PIMS

UC-View current experiment outputs: View output samples from current experiments

Summary: A user may wish to determine the nature of the output samples from recently completed (current) experiments. This might be to monitor progress or the status of projects
Importance: Desired
Priority: Desired
Use Frequency: Sometimes
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. perform UC-Search PIMS: Search data held in PIMS steps 1-4, entering details required to define a sample which is currently in use at step 3
Notes and Questions
  • output samples are defined as having a relationship to an experiment, but which are not input samples. Also, the amount must be >0.0 and the location must not be "null"

UC-View Location: View the location of a sample

Summary: A user may wish to determine the physical location of a sample(s). An example would be where the sample is to be used in an experiment
Importance: Desired
Priority: Desired
Use Frequency: Often
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. perform UC-Edit sample: Edit sample details steps 1-3
  2. view page contains sample location details
Alternative 1a
Scenario Extensions:
    Can also be achieved by searching PIMS
    1. perform UC-Search PIMS: Search data held in PIMS steps 1-4, entering details required to locate sample at step 3

UC-name: USE CASE NAME

Summary: 1-3 SENTENCES
Importance: Essential | Expected | Desired | Optional
Priority: Essential | Expected | Desired | Optional
Use Frequency: Always | Often | Sometimes | Rarely | Once
Direct Actors: ACTOR1, ACTOR2, ACTOR3
Prereq:
PRECONDITION
Main Success Scenario:
  1. STEP
  2. STEP
  3. STEP
Alternative "index"
Scenario Extensions:
    BRANCH CONDITION
    1. ALTERNATIVE STEP
    2. ALTERNATIVE STEP
    3. ALTERNATIVE STEP
Variations
TODO: Check for words of wisdom and discuss ways to improve this template.
Company Proprietary
Copyright © 2003-2004 Jason Robbins. All rights reserved. License terms. Retain this copyright statement whenever this file is used as a template.