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PIMS SRS > Use Case Suite > Crystallisation 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-New crystalization plate: Set up a new crystalization plate

Summary: An experimenter will often wish to record the details of a crystalization trial -a group of crystalization experiments.
This is a multistep process whereby the user needs to define a particulary large number of parameters.
For example: the "plate" is a multi-well plate with typically 24(6x4) or 96(12x8) wells. For each well, the user specifies a "reservoir" solution and, depending on the type of plate, one or more protein "drop"solutions.
Each drop is an individual crystalization experiment
The reservoir solutions can be provided in kit form or user-defined. A robot is often used to add the drops.
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-New experiment: Record a new experiment steps 1-6 selecting "crystalization plate"
  2. select proteins to use from list or menu(s) and click to continue
  3. see updated crystalization plate view page, with plate selection list or menu
  4. select type of plate and click to continue
  5. see updated crystalization plate view page, with screening kit selection list or menu and options for crystalization conditions
  6. select kit, options for filling order (vertical or horizontal), number of drops, if kit is to be diluted, reservoir volume, temperature and manual or robot fill and click to continue
  7. see updated crystalization plate view page, with fields to define components of "drops" and their volumes e.g. protein solutions and buffers
  8. enter details or select (from lists) and click to "view plate "
  9. see updated crystalization plate view page with editable details of each well
  10. perform UC-Submit form: Submit information in a form
Alternative 1a
Scenario Extensions:
Alternative 4a
Scenario Extensions:
    Desired protein is not included in selection list or menu
    1. click to add new protein
    2. perform UC-Add reagent: Add a new reagent to PIMS steps 3-10
    3. perform UC-New crystalization plate: Set up a new crystalization plate steps 2-10
Alternative 6a
Scenario Extensions:
    User wishes to use default conditions from a previous "saved " experiment
    1. Select to "use previous conditions" for this plate
    2. perform UC-New crystalization plate: Set up a new crystalization plate steps 7-10
Alternative 6b
Scenario Extensions:
Alternative 6c
Scenario Extensions:
    Reserviors are to be filled by a liquid handling robot
    1. select option to "robot fill" (default is manual)
    2. perform UC-Robot-generate: Generate control file for liquid-handling robot steps TO BE DETERMINED
    3. perform UC-Robot-control Send control file to a robot steps TO BE DETERMINED
    4. perform UC-New crystalization plate: Set up a new crystalization plate steps 7-10
Alternative 8a
Scenario Extensions:
Variations
  1. multiple plates may be required to be set up simultaneously, should display option to select >1 plate and subsequent pages display appropriate forms for completion
Variations
  1. a user may wish to use >one kit, for example upto 4 24-well kits with a 96-well plate. Will need to be able to define range of wells to use with each kit
Notes and Questions
  • will need link to add a new molecule (UC-Add reagent)
  • will need extensible list or drop-down menus of plate types and crystalization kits
  • need to be able to populate fields with default values from a "saved" plate. ?a protocol
  • requires calculation of volumes or concentrations

UC-Create screening solutions: Create custom screening solutions

Summary: Following a successful trial, an experimenter may wish to define custom solutions to use for the next experiment(s). This may be in order to optimize the conditions or for scaling up. Alternatively, an experimenter may wish to customize previously defined reservoir solutions (e.g. from a kit). This could be either by adding an identical amount or a gradient of a solution or ligand to selected wells.
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-New crystalization plate: Set up a new crystalization plate steps 1-5
  2. select option to "customize" screen
  3. see updated crystalization plate view page, options for customizing screen conditions
  4. define reservoir solutions from lists, select range and step size for a gradient (if required), select options for filling order (vertical or horizontal), reservoir volume, temperature, number of drops, and manual or robot fill and click to continue
  5. system performs necessary calculations of solution volumes
  6. perform UC-New crystalization plate: Set up a new crystalization plate steps 7-10
Alternative 4a
Scenario Extensions:
Variations
  1. in adding additional solutions an experimenter may wish for a uniform or gradient effect. In the latter, the range of concentrations to be added must be specified and the system perform a calculation todetermine to volume to be added to each well.
Notes and Questions
  • requires calculation of volumes or concentrations
  • 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-New multi-well experiment: Record new multi-well experiment

Summary: High and medium throughput labs will set up multiple experiments simultaneously in multi-well plates where each well contains a single experiment, in "data model" terms.
Each well will usually contain some samples in common and others which are well-specific such as PCR primers for different targets.
The plates may be set up and processed either manually or with robots.
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. perform UC-New experiment: Record a new experiment steps 1-6, selecting "multi-well" experiments
  2. select type of plate and click to continue
  3. see updated multi-well experiment view page with sample-selection list(s)
  4. select samples, from lists, to be added to all wells and click to continue
  5. see relevant multi-well experiment view page with editable details for individual wells
  6. select well-specific samples, from lists, and click to "view" plate
  7. see updated plate view page with editable details of each well
  8. perform UC-Submit form: Submit information in a form
Alternative 2a
Scenario Extensions:
Alternative 4a
Scenario Extensions:
    Desired sample does not exist in PIMS (also step 6)
    1. elect option to "add new" sample
    2. perform UC-Create sample: Create a new sample steps 3-7
    3. perform UC-New multi-well experiment: Record a new multi-well experiment steps 4-8 (or 6-8)
Alternative 7a
Scenario Extensions:
    Use robot to perform experiment set-up and processing
    1. select option to "use robot"
    2. perform UC-Robot-generate: Generate control file for liquid-handling robot steps TO BE DETERMINED
    3. perform UC-Robot-control: Send control file to a robot steps TO BE DETERMINED
    4. perform UC-Submit form: Submit information in a form
Notes and Questions
  • will need option to select "multi-well" experiments. ?single experiment as default
  • need view page for each type of plate e.g. 12 x 8 for 96 wells, or indexing system A1, A2 etc.

UC-Capture crystallization image: Capture an image from a crystallization well

Summary: The progress of a crystallization experiment is monitored by capturing microscopic images of the crystallization wells. In a large crystallization facility, plates are automatically passed to a camera. Alternatively the wells can be viewed and photographed manually.
Importance: Essential for some sites.
Priority: Desired
Use Frequency: Always
Direct Actors: Imaging robot
Main Success Scenario:
  1. imaging robot passes an image to the computer
  2. image is stored
  3. image processing algorithm scores image to assess presence and quality of crystals/precipitate
  4. score is stored with relevant image
Alternative "1a"
Scenario Extensions:
    No robot available, capture image manually
    1. user selects well to view
    2. user photographs image
    3. user instructs computer to store image
    4. perform UC-capture crystallization image: Capture an image from a crystallization well steps 3-4
Notes and Questions
  • For large sites, image capture is often provided by the manufacturers' of the robots.
    In this case, PIMS may need only to interface with it, or some PIMS partners may wish to implement improved versions.
  • A large facility may deliver one image per second, so performance is very important.
    Such a facility should be on separate hardware, so that it does not impact on general LIMS use.
  • An image processing algorithm is under development at YSBL. There should be a documented interface between the image capture routines and the image processing algorithm.

UC-View crystallization image: View an image of a crystallization well

Summary: The scientist will wish to monitor the progress of their crystallization experiments.
Importance: Essential for most sites.
Priority: Desired
Use Frequency: Often
Direct Actors: Scientist
Prereq:
The images, and details of the contents of individual wells must only be available to users with appropriate access rights.
Main Success Scenario:
  1. perform UC-View experiment: View the details of an experiment steps 1-3
  2. select image to view
  3. see selected image with the score which has been assigned to it
Alternative "1a"
Scenario Extensions:
    Can also be achieved by searching PIMS
    1. perform UC-View experiment: View the details of an experiment alternative 1a
Alternative "4"
Scenario Extensions:
    The scientist wishes to adjust the score asigned to an image
    1. perform UC-Update experiment: Update an existing experiment steps 1-3
    2. the new score is recorded
Notes and Questions
  • For large sites, image capture is often provided by the manufacturers' of the robots.
    In this case, PIMS may need only to interface with it, or some PIMS partners may wish to implement improved versions.
  • The image capture routines may be commercial ones. If so, there must be a conversion component that provides a standard interface to the PIMS viewing routines..
  • There are some large crystallization facilities, which accept proteins from other labs, so this use case must be available remotely.
  • It can takes weeks for crystals to form.

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.