Conceptual framework for a Malaria VRE in South Africa
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Transcript of Conceptual framework for a Malaria VRE in South Africa
Conceptual framework for a Malaria VRE in South Africa
Dr Heila Pienaar (UP)&
Dr Martie van Deventer (CSIR)
The Research Information Centre Stakeholder EventLondon, 23 March 2009
Timeline of investigation• South African Research Information
Services (SARIS) project – 2004– Identified virtual research
environments (VRE’s) 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 VRE’s 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 Library’s RIC, University of Purdue’s HUBzero, JISC’s myExperiment and Australia’s ARCHER e-Research toolkit
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!
Consolidated SAMI VRE components
Project management
Project management system
Proposal writing
Document management system
Generic software e.g. MS / Open Office
Real time communication
Skype, smart board, video conferences
Training / mentoring etcE-learning
system for researchers
Identification of funding sources
Identification of research area
Literature review & indexing
Identification of collaborators
Internal shared database of indexed articles
Dissemination & artifacts
Web/wiki/blog: search engines, databases; researchers & topics; funders, portals, communication, projects
Repositories: research results; experiments; literature & documents
Red: noneOrange: someYellow: all
Scientific workflow
(Collaborative) Electronic Lab book
Sophisticated instruments that generate digital information and data
Servers with data files
(Free) Data analysis software
Integrated data management system
Access to research networks & super computers; access to labs with in silico screening +
Mathematical modelling tools; numerical algorithm tools; simulation software; in silico experiments
Conclusion: the infrastructure needs much work to be converted to an integrated VRE
Demonstrator Interface
Access and authentication
Alerts and RSS feeds – may help with info overload
Library resourcesInternet resources
BL / MS RIC: Manage-ment of published info
ResearchGate: research collaboration
OPENWETWARE: Lab Notebook on Blog
myexperiment: scientific workflows
archer e-Research toolkit: data management
nanoHUB: subject gateway built on
HUBzero platform
HUBzero: access to interactive simulation
tools