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Plone panel, Naples 2007




          A new dawn for
     e-collaboration in science
                     Panelists

Marcin Davies          Telecommunications Research
                       Center, Vienna, Austria
Niels Steen Krogh      Zitelab, Denmark
Jonathan Callahan      Mazama Science, Washington
Paul Henning Krogh     University of Aarhus, Denmark
Presentations
11:05 P. H. Krogh Conceptions of collaborative
                  research processes
11:12 M. Davies    Plone for Research:
                   Requirements Revisited
11:19 J. Callahan Science in the Trenches:
                  Can Plone Help?
11:26 N. S. Krogh DANBIO
                   The Danish experience using Plone as the core
                   tool building af nation-wide research database
                   in health care (Rheumatology)

11:33 Discussion
Panel objectives
• What is needed for international scientific
  collaboration?
• What can Plone offer as an e-collaboration
  tool to support research infrastructures?
Conceptions of collaborative
   research processes
      Paul Henning Krogh
Why a special CMS application for
             Science?
• Science is forced to be done in geographical
  separation by individuals and teams
• Science, too, is under fierce pressure to increase
  its capacity to innovate – this calls for
  collaboration and efficient knowledge and
  document handling
• Science encounters, too, the problem of loosing
  the capacity to share tacit knowledge when not
  face-to-face
The CMS and the research projects
    must enter into a dialogue


CMS            Research project
General aims of a CMS
             for research projects
•   Increase research performance
•   Ensure research objectives are met
•   Aid project management
•   Stimulate exchange of ideas
•   Sharing of knowledge
•   Support teams
•   Increase visibility for insiders and outsiders
•   Bridging different domains: handle cross disciplinarity
•   Creating a common social identy – loyality to the project
    team and aims
The ecology of a research project

                                                                   S
                                                                co cie




                                             rs
                                                                  m nt




                                          e
                                       ld
                                                                    m ifi
                                                                     un c




                                     o
A research project is living




                                  eh
                                                                       ity
in an environment where it




                               ak
communicates by:




                               St
exchanging information
and knowledge and
receiving feed-back.
                                                  The project
The ICT infrastructure
delivers the communication
channels and interfaces




                                                                        lic
                                Sp




                                                                         b
                                     on




                                                                      pu
                                        s   or




                                                                   e
                                                                 Th
A new dawn for a scientist
• Chat, e-phone and meet on your common project
  portal
• Get the data of your colleague now!
• Information and literature searching – watch what
  your colleagues have watched
• Paper - and bookreading – keeping in pace with
  state of the art of her knowledge domain
• Doing experiments and investigations
• Do your analyses using rpy Plone products
• Paper co-writing on your portal
Crucial questions
Ritterskamp & Prilla (2006):
”the question of how ICT design paradigms may affect a
   system’s success within an organization usually receives
   less attention”

So, what is actually the Plone® design paradigm and is this
  particularly supportive for scientific use?

Do we have an adequate conceptual model of the scientific
  working processes?
Forschungszentrum Telekommunikation Wien


 Plone for Research:
 Requirements Revisited
 Plone Conference 2007, Naples, Italy

 Marcin Davies <davies@ftw.at>
 Telecommunications Research Center Vienna (ftw.), Austria
Introduction and motivation

  ~ 3 years of planning and development of ICT-
  platforms within research projects at the
  Telecommunications Research Center Vienna (ftw.)
  Motivation for master’s thesis about this topic [1] -
  some of the results/concepts are presented here




 [1] Davies, M: Towards a Knowledge Portal for European Research Projects,
 Vienna University of Technology, 2006 (available from: http://marcin.davies.at).
                                            2
Problem domain

 European research situation
  • Characterized by a strong fragmentation of activities,
    which is a major handicap to Europe’s competitiveness
  • Framework programmes (FPs) try to address these
    weakness by implementing large, international research
    projects:
 Scientific collaboration in general
  • A multitude of complex requirements has to be met to
    enable successful scientific knowledge sharing
     • Organizational requirements: awareness, funding, etc.
     • Technical requirements (too many to mention here...)
  • Limiting factors for cooperation:
     • Cooperative and structural factors (group diversity/size...)
     • Scientific recognition (competition, trust)
     • Technology acceptance (design challenges)
  • Scientific collaboration is not well-structured...
                                 3
Deficits of current approaches

  Organizational problems:
   • No re-usable framework
   • Late start of building ICT-infrastructure
  Technical deficits:
   • Scattered and isolated system components lead to a lack
     of user acceptance and high maintenance efforts
   • Functional deficits: missing possibilities for
      • personalization: e.g. subscriptions, notifications
      • interaction: e.g. contact search, messaging, ratings,
        comments, presence awareness, working
        environments




                                   4
Plone for scientific knowledge
portals

  Plone and Zope are fitting nicely:
   • Rich set of advanced functions out of the box
     (SmartFolders, WebDAV access, LiveSearch, etc.)
   • Rich user interface
   • Many add-on products available to implement functions of
     a scientific knowledge portal
          Custom (scientific) content types: Archetypes, ArchGenXML
      •
          Version Control: CMFEditions
      •
          Ratings: ATRatings, Subscriptions: PloneSubscription
      •
          many more...
      •
   • Highly customizable and extendable - integrates well into
     existing installations
   • Standards-based, technology-neutral
   • With Zope/ZEO: performance, flexibility, and scalability
   • Works well with other open-source components to build a
     robust infrastructure (Apache, OpenLDAP, etc.) - no
     licensing costs
                                  5
Nice, but...

  From our current experiences, building a scientific
  portal based on Plone still needs significant effort
  and expertise.
  Many components are there, but integration and
  coherence are suboptimal
  We need a common set of specific products like
  done with the Plone4Artists package
  (Plone4Scientists?)
  But before we need a:
   • Wider assessment of currently used applications
   • Refinement of requirements based on more extensive end
     user participation (and input by site integrators) etc.




                              6
What can you do?

 Please subscribe to our dedicated mailing list:
 scientific@lists.plone.org
 Participate & spread the word!




                          7
Science from the Trenches
    (Can Plone Help?)
      Jonathan Callahan
       Mazama Science
Two Views of Trenches
Workers       Management
Two Views of Science
Workers       Management
Good software makes life easier
 for workers ‘in the trenches’.
What do scientists do all day?
► Design  experiments
► Search for existing data
► Collect new data
► Assemble new and existing data
► Analyze data
► Create data visualizations
► Write results
Experimental Design
                             New Style
        Old Style

► Individual effort   ► Group  effort
► Small context       ► Big picture
► Goal =              ► Goal =
  journal article       sustained, multi-
                        decade effort (trends)
                      ► Web based tools
Data Discovery
                           New style
       Old style

► Friends           ► Friends
► Meetings          ► Meetings
                    ► Searchablerepositories
                    ► Web based tools
Data Collection
                                New style
        Old style

► Individual             ► Group
► Custom   instruments   ► Shared resources
                         ► Collaboratories
                         ► Web based tools
Data Access
                               New style
        Old style

► No versioning       ► Data repositories
► FTP from friends    ► Internet access
► No standards        ► Standard formats
                      ► Web based tools
Data Analysis
                              New style
       Old style

► Custom code         ► Institutionalsoftware
► Custom algorithms   ► Vetted algorithms
► Desktop only        ► Web based tools
Data Visualization
                               New style
         Old style

► Home  grown code     ► Institutionalsoftware
► Graphics designers   ► Scientist generated
► Desktop only         ► Web based tools
Writing up Results
                           Current style
          Old style

► Email MSWord docs   ► Email MSWord docs
► Versioning?         ► Versioning?
Can Plone help?
DANBIO
 The Danish experience using Plone as the core
tool building af nation-wide research database in
           health care (Rheumatology)

            Niels Steen Krogh, ZiteLap ApS
                   www.zitelab.dk
DANBIO: www.danbio-online.dk


• Danish, nationwide registry since 2000
• Covers 92% of all treatments
• All departments of rheumatology in Denmark
  are reporting on a regular basis
• Online registration and feedback
• Efficacy (outcome of treatment)
• Safety (drug safety)
Cohorts (the patients and the content objects)


• Biologic treatments
   – Reumatoid arthritis: 3.900 treatment series
   – Ankylosing spondylitis: 700 series
   – Psoriatic arthritis: 500 series
   – Other diagnoses: 400 series
• Early RA: 1200 pts
• Conventional treatments: 3.000 pts
• 45.000 visits (Content objects)
AIM


• To present some of the factors that we
  consider important for the success of a clinical
  registry
• A central point to remember: The user is at
  the same time
   – a researcher
   – responsible for the treatment of the
     patients
   – An emploee who must document his
     outcome (efficacy).
Why open source in life science research?


• Share methods across borders - similar to
  international research processes
• Learning processes across different academic
  fields – medicine, statistics, IT
• No licensing costs – cheaper, more flexible
• Complex, integrated solutions
• Rapid development circle
• No lock-in
DANBIO registry


• Based on Plone (2.1.2 and 3.0.1.) and other open
  source IT solutions
• Combine quality development and research in one
  registry
   – Feed back at the patient level
   – Feed back at the department level
   – Electronic CRF in clinical trials
   – Easy access to additional open source tools
       • Statistics (R-project)
       • Imaging (CDMedic-PACS X-ray server)
       • Kiosk/Touchscreens for the patient (via Firefox)
Conclusions


• Plone is usable as the core tool in the treatment of
  patients and as a research tool at the same time
• With Plone we can have very successfull
  implementations if we can have positive impact on the
  core of the academic interests of the researcher
• Plone is international and will be put into production in
  Hospitals in Norway, Sweden and Finland during the
  coming months.
• Hospitals from all over the world are welcome for
  collaboration.
• Time for Screenshots and questions
Paul Henning Krogh   A New Dawn For E Collaboration In Science
Paul Henning Krogh   A New Dawn For E Collaboration In Science

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Paul Henning Krogh A New Dawn For E Collaboration In Science

  • 1. Plone panel, Naples 2007 A new dawn for e-collaboration in science Panelists Marcin Davies Telecommunications Research Center, Vienna, Austria Niels Steen Krogh Zitelab, Denmark Jonathan Callahan Mazama Science, Washington Paul Henning Krogh University of Aarhus, Denmark
  • 2. Presentations 11:05 P. H. Krogh Conceptions of collaborative research processes 11:12 M. Davies Plone for Research: Requirements Revisited 11:19 J. Callahan Science in the Trenches: Can Plone Help? 11:26 N. S. Krogh DANBIO The Danish experience using Plone as the core tool building af nation-wide research database in health care (Rheumatology) 11:33 Discussion
  • 3. Panel objectives • What is needed for international scientific collaboration? • What can Plone offer as an e-collaboration tool to support research infrastructures?
  • 4. Conceptions of collaborative research processes Paul Henning Krogh
  • 5. Why a special CMS application for Science? • Science is forced to be done in geographical separation by individuals and teams • Science, too, is under fierce pressure to increase its capacity to innovate – this calls for collaboration and efficient knowledge and document handling • Science encounters, too, the problem of loosing the capacity to share tacit knowledge when not face-to-face
  • 6. The CMS and the research projects must enter into a dialogue CMS Research project
  • 7. General aims of a CMS for research projects • Increase research performance • Ensure research objectives are met • Aid project management • Stimulate exchange of ideas • Sharing of knowledge • Support teams • Increase visibility for insiders and outsiders • Bridging different domains: handle cross disciplinarity • Creating a common social identy – loyality to the project team and aims
  • 8. The ecology of a research project S co cie rs m nt e ld m ifi un c o A research project is living eh ity in an environment where it ak communicates by: St exchanging information and knowledge and receiving feed-back. The project The ICT infrastructure delivers the communication channels and interfaces lic Sp b on pu s or e Th
  • 9. A new dawn for a scientist • Chat, e-phone and meet on your common project portal • Get the data of your colleague now! • Information and literature searching – watch what your colleagues have watched • Paper - and bookreading – keeping in pace with state of the art of her knowledge domain • Doing experiments and investigations • Do your analyses using rpy Plone products • Paper co-writing on your portal
  • 10. Crucial questions Ritterskamp & Prilla (2006): ”the question of how ICT design paradigms may affect a system’s success within an organization usually receives less attention” So, what is actually the Plone® design paradigm and is this particularly supportive for scientific use? Do we have an adequate conceptual model of the scientific working processes?
  • 11. Forschungszentrum Telekommunikation Wien Plone for Research: Requirements Revisited Plone Conference 2007, Naples, Italy Marcin Davies <davies@ftw.at> Telecommunications Research Center Vienna (ftw.), Austria
  • 12. Introduction and motivation ~ 3 years of planning and development of ICT- platforms within research projects at the Telecommunications Research Center Vienna (ftw.) Motivation for master’s thesis about this topic [1] - some of the results/concepts are presented here [1] Davies, M: Towards a Knowledge Portal for European Research Projects, Vienna University of Technology, 2006 (available from: http://marcin.davies.at). 2
  • 13. Problem domain European research situation • Characterized by a strong fragmentation of activities, which is a major handicap to Europe’s competitiveness • Framework programmes (FPs) try to address these weakness by implementing large, international research projects: Scientific collaboration in general • A multitude of complex requirements has to be met to enable successful scientific knowledge sharing • Organizational requirements: awareness, funding, etc. • Technical requirements (too many to mention here...) • Limiting factors for cooperation: • Cooperative and structural factors (group diversity/size...) • Scientific recognition (competition, trust) • Technology acceptance (design challenges) • Scientific collaboration is not well-structured... 3
  • 14. Deficits of current approaches Organizational problems: • No re-usable framework • Late start of building ICT-infrastructure Technical deficits: • Scattered and isolated system components lead to a lack of user acceptance and high maintenance efforts • Functional deficits: missing possibilities for • personalization: e.g. subscriptions, notifications • interaction: e.g. contact search, messaging, ratings, comments, presence awareness, working environments 4
  • 15. Plone for scientific knowledge portals Plone and Zope are fitting nicely: • Rich set of advanced functions out of the box (SmartFolders, WebDAV access, LiveSearch, etc.) • Rich user interface • Many add-on products available to implement functions of a scientific knowledge portal Custom (scientific) content types: Archetypes, ArchGenXML • Version Control: CMFEditions • Ratings: ATRatings, Subscriptions: PloneSubscription • many more... • • Highly customizable and extendable - integrates well into existing installations • Standards-based, technology-neutral • With Zope/ZEO: performance, flexibility, and scalability • Works well with other open-source components to build a robust infrastructure (Apache, OpenLDAP, etc.) - no licensing costs 5
  • 16. Nice, but... From our current experiences, building a scientific portal based on Plone still needs significant effort and expertise. Many components are there, but integration and coherence are suboptimal We need a common set of specific products like done with the Plone4Artists package (Plone4Scientists?) But before we need a: • Wider assessment of currently used applications • Refinement of requirements based on more extensive end user participation (and input by site integrators) etc. 6
  • 17. What can you do? Please subscribe to our dedicated mailing list: scientific@lists.plone.org Participate & spread the word! 7
  • 18. Science from the Trenches (Can Plone Help?) Jonathan Callahan Mazama Science
  • 19. Two Views of Trenches Workers Management
  • 20. Two Views of Science Workers Management
  • 21. Good software makes life easier for workers ‘in the trenches’.
  • 22. What do scientists do all day? ► Design experiments ► Search for existing data ► Collect new data ► Assemble new and existing data ► Analyze data ► Create data visualizations ► Write results
  • 23. Experimental Design New Style Old Style ► Individual effort ► Group effort ► Small context ► Big picture ► Goal = ► Goal = journal article sustained, multi- decade effort (trends) ► Web based tools
  • 24. Data Discovery New style Old style ► Friends ► Friends ► Meetings ► Meetings ► Searchablerepositories ► Web based tools
  • 25. Data Collection New style Old style ► Individual ► Group ► Custom instruments ► Shared resources ► Collaboratories ► Web based tools
  • 26. Data Access New style Old style ► No versioning ► Data repositories ► FTP from friends ► Internet access ► No standards ► Standard formats ► Web based tools
  • 27. Data Analysis New style Old style ► Custom code ► Institutionalsoftware ► Custom algorithms ► Vetted algorithms ► Desktop only ► Web based tools
  • 28. Data Visualization New style Old style ► Home grown code ► Institutionalsoftware ► Graphics designers ► Scientist generated ► Desktop only ► Web based tools
  • 29. Writing up Results Current style Old style ► Email MSWord docs ► Email MSWord docs ► Versioning? ► Versioning?
  • 31. DANBIO The Danish experience using Plone as the core tool building af nation-wide research database in health care (Rheumatology) Niels Steen Krogh, ZiteLap ApS www.zitelab.dk
  • 32. DANBIO: www.danbio-online.dk • Danish, nationwide registry since 2000 • Covers 92% of all treatments • All departments of rheumatology in Denmark are reporting on a regular basis • Online registration and feedback • Efficacy (outcome of treatment) • Safety (drug safety)
  • 33. Cohorts (the patients and the content objects) • Biologic treatments – Reumatoid arthritis: 3.900 treatment series – Ankylosing spondylitis: 700 series – Psoriatic arthritis: 500 series – Other diagnoses: 400 series • Early RA: 1200 pts • Conventional treatments: 3.000 pts • 45.000 visits (Content objects)
  • 34. AIM • To present some of the factors that we consider important for the success of a clinical registry • A central point to remember: The user is at the same time – a researcher – responsible for the treatment of the patients – An emploee who must document his outcome (efficacy).
  • 35. Why open source in life science research? • Share methods across borders - similar to international research processes • Learning processes across different academic fields – medicine, statistics, IT • No licensing costs – cheaper, more flexible • Complex, integrated solutions • Rapid development circle • No lock-in
  • 36. DANBIO registry • Based on Plone (2.1.2 and 3.0.1.) and other open source IT solutions • Combine quality development and research in one registry – Feed back at the patient level – Feed back at the department level – Electronic CRF in clinical trials – Easy access to additional open source tools • Statistics (R-project) • Imaging (CDMedic-PACS X-ray server) • Kiosk/Touchscreens for the patient (via Firefox)
  • 37. Conclusions • Plone is usable as the core tool in the treatment of patients and as a research tool at the same time • With Plone we can have very successfull implementations if we can have positive impact on the core of the academic interests of the researcher • Plone is international and will be put into production in Hospitals in Norway, Sweden and Finland during the coming months. • Hospitals from all over the world are welcome for collaboration. • Time for Screenshots and questions