Conceptual framework for a Malaria VRE in South Africa

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Conceptual framework for a Malaria VRE in South
Africa

• Dr Heila Pienaar (UP)
• Dr Martie van Deventer (CSIR)

The Research Information Centre Stakeholder
Event London, 23 March 2009
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Timeline of investigation

• South African Research Information Services
  (SARIS) project 2004
• Identified virtual research environments (VREs)
  as an important component of current global
  research no national initiative was forthcoming
• Utilising the SERA relationship between CSIR UP
• SERA Southern Education Research Alliance
• Our aim was to establish a conceptual framework
  for a VRE
• Needed research area with much data generation
• African Centre for Gene Technologies South
  African Malaria Initiative (ACGT SAMI) was
  identified by Executives
• Malaria VRE investigation 2006 / 2007
• ACGT management agreed to participate
• Completed a day in the life research tools
  via semi-structured interviews with 20 malaria
  researchers in the SAMI network to establish
  their readiness to move to an integrated VRE

• Building of a Malaria VRE demonstrator (not a
  prototype) 2007
• Final Report July 2008 (including feedback to
  researchers). This investigation identified the
  following as priorities for our future work
• The activities carried out to perform scientific
  experiments i.e. the experimental workflow needs
  more investigation.
• The wider context in which the research is
  conducted needs to be taken into consideration.
• The current tools used by the SAMI researchers
  have to be embedded for all before they are
  expanded and enhanced by new tools.
• The collaboration needs of this specific group
  needs to drive the priorities for their VREs
  development
• The next step should be to build a prototype
  Malaria or generic VRE that can function on top
  of the South African NREN with the support of key
  South African stakeholders and by using software
  elements of other international VRE-type
  developments e.g. the British Librarys RIC,
  University of Purdues HUBzero, JISCs
  myExperiment and Australias ARCHER e-Research
  toolkit

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A day in the life

• Researchers
• Start the day with e-mail
• Largest chunk of day spent in wet lab
• Articles are written by teams
• Management of research data majority of files
  only traceable via the paper lab book
• The value of electronic lab books and managing
  their data and information properly is understood
  by all but is not currently done in any
  coherent fashion
• Much time spent on report writing .
• Whatever assistance is added should not
  contribute to their administrative burden

• Managers
• Days are planned around scheduled meetings
• Face-to-face their preferred mode of
  communication
• Spend alone time looking at research agendas,
  trends and opportunities
• Understand that the big problems associated
  with malaria could only be resolved by
  multi-disciplinary teams .

Conclusion the researchers and their managers
are ready for a changed work environment!
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Consolidated SAMI VRE components
Conclusion the infrastructure needs much work to
be converted to an integrated VRE
Red noneOrange someYellow all
Scientific workflow
(Collaborative) Electronic Lab book
Sophisticated instruments that generate digital
information and data
Access to research networks super computers
access to labs with in silico screening
Servers with data files
Integrated data management system
(Free) Data analysis software
Mathematical modelling tools numerical algorithm
tools simulation software in silico experiments
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Demonstrator Interface
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BL / MS RIC Manage-ment of published info
ResearchGate research collaboration
OPENWETWARE Lab Notebook on Blog
myexperiment scientific workflows
HUBzero access to interactive simulation tools
nanoHUB subject gateway built on HUBzero platform
archer e-Research toolkit data management