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PIMS SRS > Use Case Suite > Protein-Production Experiments 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
UC-Create Experiment Blueprint
UC-Add blueprint component
UC-Capture crystallization image
UC-View crystallization image

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 protocol: Create a new protocol

Summary: An Experimenter will sometimes need to create a new protocol (experimental method) for a particular experiment. This will be required to keep pace with technological developments, in which case, a new protocol may be created by modifying an existing protocol. Also, a completely new protocol may be required when new experiments are introduced to the laboratory.
Importance: Expected
Priority: Desired
Use Frequency: Sometimes
Direct Actors: Experimenter
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. visit "EXPERIMENTS" page
  2. select experiment type from list and click to create a new protocol
  3. see "new protocol entry" page
  4. enter new protocol name or identifier and click to continue
  5. see updated protocol "view" page
  6. select steps and enter appropriate details
  7. perform UC-Submit form: Submit information in a form
Alternative 5a
Scenario Extensions:
    A protocol with same name or identifier already exists in PIMS
    1. system displays error message and page displaying name or identifier, as entered by user, with option to change.
    2. click to cancel error and enter alternative name or identifier
    3. perform UC-Create protocol Create a new protocol steps 5-7
Variations
  1. An existing protocol can be used to create a new protocol by selecting from a list
Notes and Questions
  • will require drop-down lists of all experiment types, of existing protocols for each experiment type and of protocol steps

UC-Edit protocol: Edit a protocol

Summary: A user may sometimes may need to edit protocol details to correct errors or to match changes in laboratory practice. These will be small modifications which do not require the definition of a new protocol.
Importance: Expected
Priority: Desired
Use Frequency: Sometimes
Direct Actors: Senior scientist, PI
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. visit "EXPERIMENTS" page
  2. click to edit a protocol
  3. see list or menu to select protocol
  4. select protocol to edit
  5. see selected protocol's view page
  6. edit relevant details and click to continue
  7. perform UC-Create protocol Create a new protocol step 5 and 7
  8. see protocol's view page with modifications
  9. system logs changes including details, user Id and date

UC-View protocol: View a protocol

Summary: An experimenter may wish to view the details of a protocol.
Importance: Desired
Priority: Optional
Use Frequency: Sometimes
Direct Actors: Experimenter
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. visit "EXPERIMENTS" page
  2. click to view a protocol
  3. see selected protocol's view page
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 protocol at step 3
    2. click to display protocol's view page
    3. see selected protocol's view page
Notes and Questions
  • the format of the protocol will need to be meaningful to an experimenter, may require examples from laboratories

UC-New experiment: Record a new experiment

Summary: An experimenter will frequently need to record the details of an expeiment.
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 "PROJECTS" page and select project to use
  2. click to add a new experiment
  3. see "EXPERIMENTS" page
  4. select experiment type and protocol from lists and click to create new experiment
  5. see "new experiment entry" page with details of project, user, date, experiment type and experiment identifier
  6. click to confirm
  7. enter or select required details for samples etc.
  8. check box to indicate if result is to be recorded and enter type or select from a list
  9. perform UC-Submit form: Submit information in a form
Alternative 7a
Scenario Extensions:
    Desired sample does not exist in PIMS
    1. select option to "add new"
    2. perform UC-Create sample: Create a new sample steps 3-7
    3. perform UC-New experiment: Record a new experiment steps 7-9
Alternative 7b
Scenario Extensions:
    Sample selected defines a target which is not part of the project
    1. system displays error message and page with option to select different sample or to add selected target to the project.
    2. click to cancel error and select option
Variations
  1. Samples may or may not have barcodes
  2. A result might be a gel, a trace, a data file etc.
Notes and Questions
  • user will need to be able to view all projects for which they have access rights
  • will need link to create new sample
  • can list of "expected" samples be created for each experiment type?
  • where a gel result is to be recorded PIMS should present appropriate data-input page for details

UC-Update Experiment: Update an existing experiment

Summary: An experimenter will record the progress of an experiment by updating details such as its status and the composition of output samples, or to create a link to an image or data file. This would also be used to add a "verification" of a result such as sequencing a PCR product.
Experiment details may also need to be updated to correct errors.
Importance: Expected
Priority: Expected
Use Frequency: Sometimes
Direct Actors: Experimenter
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. visit "EXPERIMENTS" page and select experiment to update
  2. enter, edit or select required details
  3. perform UC-Submit form: Submit information in a form
Alternative 2a
Scenario Extensions:
    User wishes to add an image or data file to the experiment record
    1. click to add image or data file
    2. click to browse to file or enter "path"
    3. see file details
    4. perform UC-Submit form: Submit information in a form
    5. system records file location as link
Notes and Questions
  • where the result is a gel, trace or data file, PIMS records an appropriate new "Experiment.Gel" or "Experiment.Characterisation"

UC-Remove Experiment: Remove an experiment

Summary: An experiemnter may need to remove an experiment if e.g. it was added in unintentionally or a series defined by a workflow did not go to completion. The experiment is not removed PIMS but flagged to not be displayed
Importance: Expected
Priority: Desired
Use Frequency: Rarely
Direct Actors: Experimenter
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. visit "EXPERIMENTS" page and select experiment to remove
  2. click to remove experiment
  3. system displays warning that selected experiment is to be removed requesting confirmation
  4. click to confirm
  5. system is updated and experiment entry flagged to not be displayed

UC-View experiment: View the details of an experiment

Summary: An experimenter may wish to view the details recorded for a particular experiment. This may be to determine the quality of the results, to determine reasons for success/failure or for comparison.
Importance: Desired
Priority: Desired
Use Frequency: Sometimes
Direct Actors: Experimenter
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. visit "EXPERIMENTS" page
  2. click to select experiment to view
  3. see selected experiment's view page
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 experiment at step 3
    2. perform UC-View experiment: View the details of an experiemnt steps 2-3
Notes and Questions
  • will need details of all experiment types to be displayed in a consistent format meaningful to a researcher. Will need examples from laboratory notebooks

UC-Screen conditions: Record a screen of experimental conditions

Summary: An experimenter will frequently need to record the details of a preliminary screen of expeimental conditions. This will involve the systematic variation of the conditions to attempt to determine the optimal conditions for success.
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. perform UC-New Experiment: Record a new experiment steps 1-3
  2. select experiment type and protocol from lists and click to create new primary screen
  3. see new "primary screen" experiment entry page with details of project, user, date, experiment type and experiment identifier
  4. click to confirm
  5. enter or select required details for standard samples and conditions.
  6. enter or select required details for samples and/or conditions to be screened (varied)
  7. perform UC-Submit form: Submit information in a form
Alternative 7a
Scenario Extensions:
    Desired sample does not exist in PIMS
    1. select option to "add new"
    2. perform UC-Create sample: Create a new sample steps 3-7
    3. perform UC-New experiment: Record a new experiment steps 7-8
Alternative 7b
Scenario Extensions:
    Sample selected defines a target which is not part of the project
    1. system displays error message and page with option to select different sample or to add selected target to the project.
    2. click to cancel error and select option
Variations
  1. Sometimes a standard screen is used, e.g Hampton crystallization screens. On other occasions a screen will be designed in the light of what is known about the target.
Notes and Questions
  • user will need to be able to view all projects for which they have access rights
  • will need link to create new sample
  • can list of "expected" samples be created for each experiment type?
  • in step 5, "standard" refers to a sample or condition which is one which is to remain constant for each experiment
  • in step 6, "screened" refers to a sample or condition which is one which is to be varied
  • Screen design for crystallization optimisation is an active topic of research. PIMS cannot commit to a particular algorithm, but must provide an interface which makes it simple to write plug-ins.

UC-Create Experiment Blueprint: Create a new Experiment Blueprint

Summary: A user will sometimes wish to create a new Experiment Blueprint as a means of representing experimental objectives.
An example of an objective might be "to work on a particular domain of a target". The contents of the Experiment Blueprint are called Blueprint components.
Importance: Expected
Priority: Desired
Use Frequency: Sometimes
Prereq:
User must belong to a user group with appropriate access rights
Main Success Scenario:
  1. visit "Experiment Blueprint" page
  2. click to create "new"
  3. see new Experiment Blueprint entry page with details of project, user and date
  4. enter required details: "local name, common name, why chosen" and other details as appropriate
  5. click to continue
  6. see updated entry page with option to add Blueprint components
  7. perform Submit form: Submit information in a form
Alternative 7a
Scenario Extensions:
    add Blueprint component
    1. perform UC-Add blueprint component steps 4-9

UC-Add blueprint component: Add a Blueprint component to an Experiment blueprint

Summary: A user will need to add Blueprint components to an Experiment Blueprint.
These are the targets, domains or fragments of targets and non-polymer molecules, which are to be studied.
Importance: Expected
Priority: Desired
Use Frequency: Sometimes
Prereq:
User must belong to a user group with appropriate access rights
Experiment Blueprint must exist in PIMS
Main Success Scenario:
  1. visit "Experiment Blueprint" page
  2. select Experiment Blueprint to use
  3. see appropriate Experiment Blueprint view page
  4. select option to add Blueprint component
  5. see new Blueprint component entry page with details of relevant Experiment Blueprint
  6. enter required details: "component type, common name, why chosen" and other details as appropriate
  7. select molecule to store sequence (polymer) or structure (non-polymer) (optional)
  8. perform UC-Submit form: Submit information in a form
  9. system records details for Blueprint component and relevant links
Alternative 2a
Scenario Extensions:
Alternative 7a
Scenario Extensions:
    molecule does not exist in PIMS
    1. click to add new molecule
    2. perform UC-Add new target: Add a new target to PIMS steps 3-5
    3. system records new molecule details with link to Blueprint component
Alternative 8a
Scenario Extensions:
    blueprint component is a target domain
    1. select target and define boundaries (beginning and end residue numbers in target) and enter a name for domain
    2. perform UC-Add blueprint component: Add a Blueprint component to an Experiment blueprint steps 8-9

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.