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PIMS SRS > Use Case Suite > Reagent management 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-Add reagent: Add a new reagent to PIMS

Summary: A user will need to record details of new reagents which can be can be of different types: molecular component, cell, substance etc. This would be required when an experiment type is recorded for the first time or an existing protocol is modified.
Where the user wishes to track a reagent, a barcode can be added
Will be particularly important in the initial stages.
Importance: Expected
Priority: Expected
Use Frequency: Sometimes
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. Visit "REAGENTS" page or menu
  2. click to add new reagent of relevant "type"
  3. see appropriate "new reagent" entry page
  4. select reagent from searchable reference data sets and click to add reagent details
  5. see updated new reagent form with editable details from reference data set
  6. click to confirm
  7. see updated new reagent form with option to select supplier details
  8. select supplier details from searchable reference data set
  9. select holder and/or container and location
  10. perform Submit form: Submit information in a form
Alternative 4a
Scenario Extensions:
    Reagent is not included in reference data set
    1. enter required reagent details manually and check box to add details to reference data set if required
    2. click to continue
    3. perform UC-Add reagent: Add a new reagent to PIMS steps 5-10
Alternative 4b
Scenario Extensions:
    Reagent is not included in reference data set and is a "polymer" molecular component
    1. click to add new molecular component selecting options for polymer type e.g. DNA, protein
    2. see import page
    3. perform UC-Add new target to PIMS: Add new target to PIMS steps 4-5
    4. see updated "new reagent" entry page
    5. check box to add details to reference data set if required and click to continue
    6. perform UC-Add reagent: Add a new reagent to PIMS steps 5-10
Alternative 8a
Scenario Extensions:
    Supplier is not included in reference data set
    1. enter supplier and location details for reagent
    2. check box to add details to reference data set if required and click to continue
    3. see updated "new reagent" entry page
    4. perform UC-Add reagent: Add a new reagent to PIMS steps 9-10
Alternative 10a
Scenario Extensions:
    Reagent container or holder has a unique barcode
    1. perform UC-Scan barcode: Scan a barcode Alternative 1a steps 2-5
    2. perform UC-Add reagent: Add a new reagent to PIMS step 10
Variations
  1. forms with different fields will be displayed according to reagent type
Notes and Questions
  • will benefit from pre-populated but extensible reference data sets for reagents (including hazard information and component type -detergent, precipitant, primer etc.), containers and suppliers

UC-Edit reagent: Edit reagent details

Summary: A user may need to edit the details recorded for a reagent. This would be if incomplete or incorrect details were entered in UC-Add reagent: Add a new reagent to PIMS. Also, if local details such as location were changed. Or when a modification of an existing molecule is made or used.
Importance: Desired
Priority: Desired
Use Frequency: Sometimes
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. Visit "REAGENTS" page or menu
  2. select reagent from searchable list and click to edit
  3. see reagent's view page
  4. edit appropriate fields
  5. perform Submit form: Submit information in a form
Variations
  1. a new reagent can be created from an existing one in this way
Notes and Questions
  • will require option to "save as"

UC-New container: Add a new container to PIMS

Summary: An experimenter may need to add a new type of container or holder to PIMS. Container types include tubes, plates, flasks etc.
This would necessary be if new container types were developed or introduced to the lab or if the supplier was changed.
Importance: Desired
Priority: Desired
Use Frequency: Rarely
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. visit the appropriate page and click to add new container
  2. enter required details
  3. perform Submit form: Submit information in a form
Variations
  1. a new container can be created from an existing one e.g. where just supplier details are to be changed
Notes and Questions
  • require extensible, pre-populated "dictionary" of container types
  • will require option to "save as" for modifying an existing container

UC-View reagents: View list of reagents in PIMS

Summary: An experimenter may wish to view a list of all reagents recorded in PIMS. This might be for inventory purposes.
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, entering or selecting details required to identify all reagents
Variations
  1. could also be used for containers and holders
Notes and Questions
  • in PIMS, reagents are samples which are not associated with experiments , except for the ImportSample experiment
  • list returned should contain clickable links to individual reagent view pages
  • only include reagents where "Location is not null" and "current amount is not zero"

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.
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Copyright © 2003-2004 Jason Robbins. All rights reserved. License terms. Retain this copyright statement whenever this file is used as a template.