Project Information

Project:	PIMS
Interviewer(s):	Chris Morris and Susy Griffiths
Interviewee(s):	Steve Prince and Miroslav Papiz
Date of Interview:	28-06-04
Interview Location:	Steve's office UMIST
Related Documents:	Project proposal > Target audience and benefits Glossary

Process impact: Planning questions for interviews with stakeholders is key to effective requirements gathering. Good requirements are needed to build the right system. These notes should be kept as part of the documentation on user needs are referred to when the software requirements specification is written or updated.

Interview Questions and Answers

Any previous experience with a LIMS system?

Steve -none
Miroslav -has used "mole"

Prioritize scientific goals in use-case-suite:

Target selection and Bioinformatics (see note 1 below)
Project management
Sample tracking
Experiment/protocol management
Logging in and out
Usr account management
Interfacing to laboratory equipment (see note 2)
Reporting
Workflow tools (see note 3)
Mobile data collection (see note 4)
Reagent management
Scheduling
Data mining and visualisation
Installability

notes

1. Target selection and Bioinformatics (This may be different at other MPSI sites)
1. target suggestions given to Mark Samson (Oxford)
2. performs target validation - check of annotation, GC content, suitability for expression in E.coli existence of close homologues with solved structure
3. target selected
4. grouped according to function
5. primer design
2. Interfacing to laboratory equipment
-high priority request for capability to store and retrieve robot control files
-noted likelihood that individual consortium sites will use equipment from different manufacturers and so a tool to translate control files for use on all equipment would be desirable
3. Workflow tools
identified instances where workflow will need to be modified to allow inclusion of additional steps to standard workflow
e.g. Where a purification step is not effective and requires further e.g. column purification(s)
4. Mobile data collection
Availability of bar-coding is essential since all samples, from DNA plasmids to crystals, may be transferred between sites and so will need to be reliably tracked

What requirements do you have for a LIMS?

1. MP defined two separate types of information:
   -information which is essential to the workflow e.g. Sequence details, primers etc
   -desirable information e.g. ??
2. SP requested that nomenclature for membrane proteins from the Membrane Transport Protein Classification Database TC_DB be recorded, as this is a reliable source of functional information
   -CM suggested a link to this could be provided from the PIMS interface
   -also, refer to data model html file for fields supported in the "Target" table
3. SP requires LIMS which is "additive and not deletable" and allows storage of all experimental details including errors
4. SP raised concerns about the "precision" of stored information requesting that the maximum level of detail is required
   examples are:
   -EM images rather than lower resolution JPEG images
   -Sequencing gel chromas rather than a text file containing the base-calls made by the analysis software used
   -Raw data rather than processed results
5. MP requires to be able to track the progress of a target visually
6. A requirement for archiving was suggested whereby information for targets which are no longer being worked on could be removed from the main interface
7. SP requested storage of diffraction images acquired at the beamline

What level of confidentiality is required?

SP & MP This area requires further discussion between the consortium members.
The physical samples will be mobile between the member sites and so access to target and experimental information will need to be freely available.
There is also the likelihood of industrial collaborations where access to certain areas of the LIMS will need to be confidential.

What do you see as your immediate requirements?

SP requested a LIMS for immediate use on the project start date of July 1st 2004.
CM stated that the PIMS project proposal is to advise customers to use the EBI target tracker with a series of spreadsheets
SP raised concerns regarding te confidentiality of such a repository

Other Interview Notes

ADDITIONAL NOTES AND ACTION POINTS:

• Electrophysiology/transport-type experiments were described which form the basis of functional assays for membrane transport proteins.
  The development of such novel transport assays is part of the MPSI SpoRT application. This highlights some inadequacies in the protein production data model underlying PIMS.
  Firstly, electrophysiology experiments are unlikely to be adequately describe using the existing experiment types.
  Secondly, such experiments usually for part of a time-series which may require adjustments to the data model.


• Request a copy of MPSI SPoRT application to determine if there are likely to be any additional novel experiment types for consideration.
  RECEIVED 1-7-04
  Emphasises requirements as listed above and some in addition:
  

  PIMS is required to document and support:

  • the production of multiple expression constructs in parallel for each protein target. Use of a liquid handling robot for many steps.
    Anne Pajon said:"Concerning the construct where multiple variations of the same target are to be created, the way it is done for the moment is:
    - You have to create one construct for each variation
    - Then, you have to link this construct to a new molecule that stores the sequence of this particular construct
    - And finally, you have to link this contruct to the molecule that stores the sequence of your target (referTo link between Construct (MolComponent) and Molecule)
    or your BlueprintComponent."
    See diagram
  • the parallel testing of protein expression with a variety of host strains and expression conditions
  • use of 96-well plate-based fluorescence assays to determine sub-cellular location of expressed protein
  • electronic data capture from "Agilent 2100 bioanalyzer and Protein LabChips" used to monitor protein purification
  • storage, and accessible to all consortium members, of all data on preparation, purification, solubilisation and protocols
  • support all elements of x-ray data collection including crystal screening and MAD techniques
  • CD (circular dichroism) and functional assays
  • negative stain EM for mono-dispersity (alternative to DLS)
  • rational screening based on strategy from Itawa's lab (IC)
  • automated HTP crystallisation using crystallisation robots
  • generation and use of monoclonal antibodies (mabs) for selected targets
  • Use of CCP4 suite of programs
  • EM of 2D crystals with parallel testing of up to 150 combinations of conditions/proteins
  • EM data collection and image processing


• Request URLs or names for primer design tools/software currently used
  RECEIVED from SP 1-7-04:
  "Colleagues in Leeds have specifically gained funds to use Invitrogen Vector-NTI software
  I guess othere people might use different software (the above is for use with the Invitrogen Gateway Cloning technology)
  but Vector-NTI should certainly be supported by the LIMS"


• Request copies of electrophysiology-type experiment protocols to assist in defining new experiments for data model
  RECEIVED 5-7-04 from MP book chapter:
  Ward, A et al.(2000) in Membrane Transport -A practical Approach (Baldwin, S.A., ed.), pp141-146, OUP, Oxford
  contains details of protocols used in Leeds specifically:
  PROTOCOL 7:Counterflow assay for activity of reconstituted GalP(His)₆ protein
  PROTOCOL 6A: Reconstitution of detergent-solubilized membrane proteins into E.coli liposomes by detergent dilution


• Confirm URL for TC_DB site as: http://saier-144-164.ucsd.edu/tcdb/
  Confirmed 1-7-04


• Send data model HTML help file 30-6-04