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PIMS SRS > Use Case Suite > Target 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 new target: Add a new target to PIMS

Summary: Subsequent to bioinformatic screening and selection, user instructs PIMS to record details for a new target.
Achieved by entering a unique identifier code for the target in a remote database (e.g.Swiss-Prot accession number). The system then records the retrieved information.
Importance: Essential
Priority: Essential
Use Frequency: Often
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. visit "TARGETS" page
  2. click to add new target
  3. see target import page
  4. enter identifier code and select database
  5. perform UC-Submit form: Submit information in a form
Alternative 4a
Scenario Extensions:
    Target with same database identifier already exists in PIMS
    1. system displays error appropriate error message, displaying target identifier, entered by user, with target summary from PIMS.
    2. click to cancel error
    3. see "TARGETS" page
Alternative 4b
Scenario Extensions:
    Database identifier does not exist in selected database
    1. system re-displays target import page, with error message displaying incorrect identifier and database name
    2. click to cancel error
    3. perform UC-Add new target: Add a new target to PIMS steps 4-5
Notes and Questions
  • will require drop-down list of available database connections
  • will need page from which all targets are accessble
  • will also need to create a "molecule" in the database for the DNA sequence
  • use EBI web services WSDbfetch to retrieve target information
  • what about potential targets? Can they be recorded as reagents initially and "upgraded" to targets when required?
  • may need to be able to add multiple targets simultaneously
  • can we upload target details stored locally and have option to "paste" a sequence?

UC-Edit target: Edit target details

Summary: User may often need to edit/update target details. e.g.some attributes need to be entered manually such as:
'Why the target was chosen' and 'local name'
Importance: Expected
Priority: Expected
Use Frequency: Often
Prereq:
The target exists in PIMS
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. visit "TARGETS" page
  2. click to select target to edit
  3. see the target's individual view page
  4. edit appropriate fields
  5. perform UC-Submit form: Submit information in a form
Notes and Questions
  • some attributes cannot be changed?
    • Alternative 1b Scenario Extensions:

UC-View target status: View the status of a target

Summary: User will often wish to view the progress of a target in the protein production process.
Importance: Expected
Priority: Desired
Use Frequency: Often
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. visit "TARGETS" page
  2. click to select target to view progress
  3. see the target's progress
Variations
  1. multiple targets can be selected for viewing simultaneously by clicking
  2. multiple targets can be selected for viewing simultaneously according to defined 'groupings'
Notes and Questions
  • will need representation of status -like the EBI target tracker view, where progress is represented as steps in a workflow with colour-coded status

UC-Add citation: Add details of a citation to a target

Summary: A user may wish to add details of relevant publications to the target. May be part of target selection procedure
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-Edit target: Edit target details steps 1-3
  2. click to add citation of appropriate type
  3. see new citation data entry page
  4. enter required details
  5. perform UC-Submit form: Submit information in a form steps 1-3
  6. system records citation information for target
  7. see updated target view page
Variations
  1. a citation can be from a journal, thesis, conference or book
Notes and Questions
  • already avaiable for Molecule.Molecule, People.Person and Protocol
  • could PIMS create a link to the full text or PDF where available?

UC-Find citations: Find citations relating to a target

Summary: A user may wish to find publications relevant to a target.
Usually involves manual search of approriate site e.g. PubMed
Importance: Desired
Priority: Desired
Use Frequency: Sometimes
Prereq:
User must belong to a user group with appropriate acceAlternative 1b Scenario Extensions: ss rights
Main Success Scenario:
  1. TODO
Notes and Questions
  • Can this be automated? e.g. the Entrez Utilities ELink tool can be used to define a URL to retrieve PubMed ids for a given sequence id (GI number)
    The retrieved pubmed id's can then be used to create a second URL to retrieve links to the full text article(s), use "cmd=prlinks" in URL
  • see also NCBI SOAP interface for eutils

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.